Significance of the V-type ATPase for the adaptation to stressful growth conditions and its regulation on the molecular and biochemical level

Integrated proteomics, transcriptomics, and metabolomics offer novel insights into Cd resistance and accumulation in Poa pratensis

Kentucky bluegrass (Poa pratensis L., KB) demonstrates superior performance in both cadmium (Cd) accumulation and tolerance; however, the regulatory mechanisms and detoxification pathways in this species remain unclear. Therefore, phenotype, root ultrastructure, cell wall components, proteomics, transcriptomics, and metabolomics were analyzed under the hydroponic system to investigate the Cd tolerance and accumulation mechanisms in the Cd-tolerant KB variety 'Midnight (M)' and the Cd-sensitive variety 'Rugby II (R)' under Cd stress. The M variety exhibited higher levels of hydroxyl and carboxyl groups as revealed by Fourier transform infrared spectroscopy spectral analysis. Additionally, a reduced abundance of polysaccharide degradation proteins was observed in the M variety. The higher abundance of glutathione S-transferase and content of L-cysteine-glutathione disulfide and oxidized glutathione in the M variety may contribute to better performance of the M variety under Cd stress. Additionally, the R variety had an enhanced content of carboxylic acids and derivatives, increasing the Cd translocation capacity. Collectively, the down-regulation of cell wall polysaccharide degradation genes coupled with the up-regulation of glutathione metabolism genes enhances the tolerance to Cd stress in KB. Additionally, lignification of the endodermis and the increase in carboxylic acids and derivatives play crucial roles in the redistribution of Cd in KB.

The A subunit of vacuolar H+-ATPase gene (CmVHA-A) plays opposite roles in plant growth and drought tolerance of chrysanthemum under different growing conditions

As the most prominent proton pumps in plants, vacuolar H+-ATPases (VHAs) comprise multiple subunits that are important for physiological processes and stress tolerance in plants. However, few studies on the roles of subunit genes of VHAs in chrysanthemum have been reported to date. In this study, the gene of A subunit of V-ATPase in chrysanthemum (CmVHA-A) was cloned and identified. CmVHA-A was conserved with VHA-A proteins from other plants. Expression analysis showed that CmVHA-A was highly expressed in most tissues of chrysanthemum except for the flower bud, and was readily induced by polyethylene glycol (PEG) treatment. Functional analysis demonstrated that CmVHA-A exerted a negative influence on the growth and development of shoot and root of chrysanthemum under normal conditions. RNA-sequencing (RNA-seq) analysis revealed the possible explanations for phenotypic differences between transgenic and wild-type (WT) plants. Under drought conditions, CmVHA-A positively affected the drought tolerance of chrysanthemum by enhancing antioxidase activity and alleviating photosynthetic disruption. Overall, CmVHA-A plays opposite roles in plant growth and drought tolerance of chrysanthemums under different growing conditions.

From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance

Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.

Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment

Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial lifecycles involving growth and dormancy alternation. This study explores genetic controls and molecular mechanisms enabling S. uncinata to cope with seasonality of the Antarctic environment. We analysed the seasonal transcriptome dynamics of S. uncinata collected monthly from February 2015 to January 2016 in King George Island, Antarctica. Findings indicate that genes involved in plant growth were predominantly upregulated in Antarctic summer, while those associated with protein synthesis and cell cycle showed marked expression during the winter-to-summer transition. Genes implicated in cellular stress and abscisic acid signalling were highly expressed in winter. Further, validation included a comparison of the Antarctic field transcriptome data with controlled environment simulation of Antarctic summer and winter temperatures, which revealed consistent gene expression patterns in both datasets. This proposes a seasonal gene regulatory model of S. uncinate to understand moss adaptation to extreme environments. Additionally, this data set is a valuable resource for predicting genetic responses to climatic fluctuations, enhancing our knowledge of Antarctic flora's resilience to global climate change.

Exogenous Nitric Oxide Alleviates Water Deficit and Increases the Seed Production of an Endemic Amazonian Canga Grass

Open pit mining can cause loss in different ecosystems, including damage to habitats of rare and endemic species. Understanding the biology of these species is fundamental for their conservation, and to assist in decision-making. Sporobolus multiramosus is an annual grass endemic to the Amazon canga ecosystems, which comprise rocky outcrop vegetation covering one of the world's largest iron ore reserves. Here, we evaluated whether nitric oxide aids S. multiramosus in coping with water shortages and examined the physiological processes behind these adaptations. nitric oxide application improved the water status, photosynthetic efficiency, biomass production, and seed production and germination of S. multiramosus under water deficit conditions. These enhancements were accompanied by adjustments in leaf and root anatomy, including changes in stomata density and size and root endodermis thickness and vascular cylinder diameter. Proteomic analysis revealed that nitric oxide promoted the activation of several proteins involved in the response to environmental stress and flower and fruit development. Overall, the results suggest that exogenous nitric oxide has the potential to enhance the growth and productivity of S. multiramosus. Enhancements in seed productivity have significant implications for conservation initiatives and can be applied to seed production areas, particularly for the restoration of native ecosystems.

Arabidopsis thaliana Early Foliar Proteome Response to Root Exposure to the Rhizobacterium Pseudomonas simiae WCS417

Pseudomonas simiae WCS417 is a plant growth-promoting rhizobacterium that improves plant health and development. In this study, we investigate the early leaf responses of Arabidopsis thaliana to WCS417 exposure and the possible involvement of formate dehydrogenase (FDH) in such responses. In vitro-grown A. thaliana seedlings expressing an FDH::GUS reporter show a significant increase in FDH promoter activity in their roots and shoots after 7 days of indirect exposure (without contact) to WCS417. After root exposure to WCS417, the leaves of FDH::GUS plants grown in the soil also show an increased FDH promoter activity in hydathodes. To elucidate early foliar responses to WCS417 as well as FDH involvement, the roots of A. thaliana wild-type Col and atfdh1-5 knock-out mutant plants grown in soil were exposed to WCS417, and proteins from rosette leaves were subjected to proteomic analysis. The results reveal that chloroplasts, in particular several components of the photosystems PSI and PSII, as well as members of the glutathione S-transferase family, are among the early targets of the metabolic changes induced by WCS417. Taken together, the alterations in the foliar proteome, as observed in the atfdh1-5 mutant, especially after exposure to WCS417 and involving stress-responsive genes, suggest that FDH is a node in the early events triggered by the interactions between A. thaliana and the rhizobacterium WCS417. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Impacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection

Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.

Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system

Manipulation of host phenotypes by parasites is hypothesized to be an adaptive strategy enhancing parasite transmission across hosts and generations. Characterizing the molecular mechanisms of manipulation is important to advance our understanding of host-parasite coevolution. The trematode (Levinseniella byrdi) is known to alter the colour and behaviour of its amphipod host (Orchestia grillus) presumably increasing predation of amphipods which enhances trematode transmission through its life cycle. We sampled 24 infected and 24 uninfected amphipods from a salt marsh in Massachusetts to perform differential gene expression analysis. In addition, we constructed novel genomic tools for O. grillus including a de novo genome and transcriptome. We discovered that trematode infection results in upregulation of amphipod transcripts associated with pigmentation and detection of external stimuli, and downregulation of multiple amphipod transcripts implicated in invertebrate immune responses, such as vacuolar ATPase genes. We hypothesize that suppression of immune genes and the altered expression of genes associated with coloration and behaviour may allow the trematode to persist in the amphipod and engage in further biochemical manipulation that promotes transmission. The genomic tools and transcriptomic analyses reported provide new opportunities to discover how parasites alter diverse pathways underlying host phenotypic changes in natural populations.

Involvement of NO in V-ATPase Regulation in Cucumber Roots under Control and Cadmium Stress Conditions

Nitric oxide (NO) is a signaling molecule that participates in plant adaptation to adverse environmental factors. This study aimed to clarify the role of NO in the regulation of vacuolar H+-ATPase (V-ATPase) in the roots of cucumber seedlings grown under control and Cd stress conditions. In addition, the relationship between NO and salicylic acid (SA), as well as their interrelations with hydrogen sulfide (H2S) and hydrogen peroxide (H2O2), have been verified. The effect of NO on V-ATPase was studied by analyzing two enzyme activities, the expression level of selected VHA genes and the protein level of selected VHA subunits in plants treated with a NO donor (sodium nitroprusside, SNP) and NO biosynthesis inhibitors (tungstate, WO42- and N-nitro-L-arginine methyl ester, L-NAME). Our results indicate that NO functions as a positive regulator of V-ATPase and that this regulation depends on NO generated by nitrate reductase and NOS-like activity. It was found that the mechanism of NO action is not related to changes in the gene expression or protein level of the V-ATPase subunits. The results suggest that in cucumber roots, NO signaling interacts with the SA pathway and, to a lesser extent, with two other known V-ATPase regulators, H2O2 and H2S.

Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure

The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F₄₂₀ content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.

Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley

Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (F_VF_M, and F_VF₀) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.

Transcriptome assessment in 'Red Globe' grapevine zygotic embryos during the cooling and warming phase of the cryopreservation procedure

Cryopreservation has the potential for long-term germplasm storage. The metabolic pathways and gene regulation involved in cryopreservation procedures are still not well documented. Hence, the genetic expression profile was evaluated using RNA-Seq in zygotic embryos of grapevines subjected to cryopreservation by vitrification. Sequencing was performed on the Illumina NextSeq 500. The average alignment of reads was 96% against the reference genome. The expression profiles showed 229 genes differentially expressed (186 repressed and 46 induced). The main biological processes showing upregulated enrichment were related to nucleosome assembly, while downregulated processes were related to organ growth. The most highly repressed processes were associated with the organization of the cell wall and membrane components. The unnamed protein product and 17.3 kDa class II heat shock protein (HSP) were highly induced, while ATPase subunit 1 and expansin-A1 were repressed. The response to the cooling and warming process during cryopreservation probably indicates that the changes occurring in transcription may be related to epigenetics. In addition, the cell exhibits an increase in the reserve of nutrients while seeking to survive modestly using available energy and pausing the plant's development. Additionally, energy containment occurred to cope with the stress caused by the treatment where deactivation of components of the cell membrane was observed, possibly due to changes in fluidity caused by alterations in temperature.

Impacts of 2-bromoethanesulfonic sodium on methanogenesis: Methanogen metabolism and community structure

Production of medium-chain carboxylic acids (MCCAs) by chain elongation (CE) presents a competitive alternative to conventional products of methane in anaerobic digestion treating organic waste streams, considering energy recovery, economic, and environmental profits. However, the system stability and performance largely rely on the selective suppression of methanogens while stimulation of CE bacteria. Commercial inhibitors such as 2-bromoethanesulfonic sodium (BES) was shown to be effective, but controversial conclusions exist on its inhibition characteristics and the inhibition mechanism remains unclear. Therefore, this study systematically investigated the responses of methanogenesis in granular sludge to various BES levels, focusing on methane production, methanogenic pathway, dynamic populations, electron transport and energy metabolism. Results showed that compared with the control, 3.0 g/L BES was sufficient to induce a 72.9% reduced level on accumulative methane production by the end of 4 cycles (28 days), which was likely to be attributed to the significantly suppressed metabolic pathways and intracellular regulations. Specifically, BES suppressed the electron transport via unproper electron carriers and reduced electron amount as indicated by the decreased level of enzymes and genes involved such as coenzyme F₄₂₀, CO dehydrogenase and NADH:ubiquinone reductase (H⁺-translocating). Moreover, BES regulated the intracellular energy metabolism, leading to the impeded ATP synthesis but enhanced ATP consumption as evidenced by the variations on the activity or abundance of acetate kinase, A1Ao-ATP synthase, nitrogenase and ATP citrate synthase. Additionally, BES enriched hydrogenotrophic methanogenesis over acetoclastic one as supported by variations on the archaeal community structures and regulations of differentially expressed genes involved. Moreover, BES also reduced the contents of both protein and carbohydrate in extracellular polymeric substances (EPS). This study is expected to enhance understanding of BES contribution to methanogenesis inhibition but MCCAs production in CE bioreactors.

Drought stress tolerance mechanisms and their potential common indicators to salinity, insights from the wild watermelon (Citrullus lanatus): A review

Climate change has escalated the effect of drought on crop production as it has negatively altered the environmental condition. Wild watermelon grows abundantly in the Kgalagadi desert even though the environment is characterized by minimal rainfall, high temperatures and intense sunshine during growing season. This area is also characterized by sandy soils with low water holding capacity, thus bringing about drought stress. Drought stress affects crop productivity through its effects on development and physiological functions as dictated by molecular responses. Not only one or two physiological process or genes are responsible for drought tolerance, but a combination of various factors do work together to aid crop tolerance mechanism. Various studies have shown that wild watermelon possess superior qualities that aid its survival in unfavorable conditions. These mechanisms include resilient root growth, timely stomatal closure, chlorophyll fluorescence quenching under water deficit as key physiological responses. At biochemical and molecular level, the crop responds through citrulline accumulation and expression of genes associated with drought tolerance in this species and other plants. Previous salinity stress studies involving other plants have identified citrulline accumulation and expression of some of these genes (chloroplast APX, Type-2 metallothionein), to be associated with tolerance. Emerging evidence indicates that the upstream of functional genes are the transcription factor that regulates drought and salinity stress responses as well as adaptation. In this review we discuss the drought tolerance mechanisms in watermelons and some of its common indicators to salinity at physiological, biochemical and molecular level.

Plant salt response: Perception, signaling, and tolerance

Salt stress is one of the significant environmental stressors that severely affects plant growth and development. Plant responses to salt stress involve a series of biological mechanisms, including osmoregulation, redox and ionic homeostasis regulation, as well as hormone or light signaling-mediated growth adjustment, which are regulated by different functional components. Unraveling these adaptive mechanisms and identifying the critical genes involved in salt response and adaption are crucial for developing salt-tolerant cultivars. This review summarizes the current research progress in the regulatory networks for plant salt tolerance, highlighting the mechanisms of salt stress perception, signaling, and tolerance response. Finally, we also discuss the possible contribution of microbiota and nanobiotechnology to plant salt tolerance.

iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean

Adzuki bean is an important legume crop due to its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. However, little information is available about the genetic control of drought tolerance during seed germination in adzuki bean. In this study, some differential expression proteins (DEPs) were identified during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean using iTRAQ method. A total of 2834 proteins were identified in the germinating seeds of these two adzuki beans. Compared with the variety 17033, 87 and 80 DEPs were increased and decreased accumulation in variety 17235 under drought, respectively. Meanwhile, in the control group, a few DEPs, including 9 up-regulated and 21 down-regulated proteins, were detected in variety 17235, respectively. GO, KEGG, and PPI analysis revealed that the DEPs related to carbohydrate metabolism and energy production were significantly increased in response to drought stresses. To validate the proteomic function, the ectopic overexpression of V-ATPase in tobacco was performed and the result showed that V-ATPase upregulation could enhance the drought tolerance of tobacco. The results provide valuable insights into genetic response to drought stress in adzuki bean, and the DEPs could be applied to develop biomarkers related to drought tolerant in adzuki bean breeding projects.

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Simple Summary

Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses.

Abstract

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.

The Adaptation and Tolerance of Major Cereals and Legumes to Important Abiotic Stresses

Abiotic stresses, including drought, extreme temperatures, salinity, and waterlogging, are the major constraints in crop production. These abiotic stresses are likely to be amplified by climate change with varying temporal and spatial dimensions across the globe. The knowledge about the effects of abiotic stressors on major cereal and legume crops is essential for effective management in unfavorable agro-ecologies. These crops are critical components of cropping systems and the daily diets of millions across the globe. Major cereals like rice, wheat, and maize are highly vulnerable to abiotic stresses, while many grain legumes are grown in abiotic stress-prone areas. Despite extensive investigations, abiotic stress tolerance in crop plants is not fully understood. Current insights into the abiotic stress responses of plants have shown the potential to improve crop tolerance to abiotic stresses. Studies aimed at stress tolerance mechanisms have resulted in the elucidation of traits associated with tolerance in plants, in addition to the molecular control of stress-responsive genes. Some of these studies have paved the way for new opportunities to address the molecular basis of stress responses in plants and identify novel traits and associated genes for the genetic improvement of crop plants. The present review examines the responses of crops under abiotic stresses in terms of changes in morphology, physiology, and biochemistry, focusing on major cereals and legume crops. It also explores emerging opportunities to accelerate our efforts to identify desired traits and genes associated with stress tolerance.

Salinity tolerance mechanisms and their breeding implications

BACKGROUND

The era of first green revolution brought about by the application of chemical fertilizers surely led to the explosion of food grains, but left behind the notable problem of salinity. Continuous application of these fertilizers coupled with fertilizer-responsive crops make the country self-reliant, but continuous deposition of these led to altered the water potential and thus negatively affecting the proper plant functioning from germination to seed setting.

MAIN BODY

Increased concentration of anion and cations and their accumulation and distribution cause cellular toxicity and ionic imbalance. Plants respond to salinity stress by any one of two mechanisms, viz., escape or tolerate, by either limiting their entry via root system or controlling their distribution and storage. However, the understanding of tolerance mechanism at the physiological, biochemical, and molecular levels will provide an insight for the identification of related genes and their introgression to make the crop more resilient against salinity stress.

SHORT CONCLUSION

Novel emerging approaches of plant breeding and biotechnologies such as genome-wide association studies, mutational breeding, marker-assisted breeding, double haploid production, hyperspectral imaging, and CRISPR/Cas serve as engineering tools for dissecting the in-depth physiological mechanisms. These techniques have well-established implications to understand plants' adaptions to develop more tolerant varieties and lower the energy expenditure in response to stress and, constitutively fulfill the void that would have led to growth resistance and yield penalty.

Current progress in plant V-ATPase: From biochemical properties to physiological functions

Vacuolar-type adenosine triphosphatase (V-ATPase, VHA) is a highly conserved, ATP-driven multisubunit proton pump that is widely distributed in all eukaryotic cells. V-ATPase consists of two domains formed by at least 13 different subunits, the membrane peripheral V₁ domain responsible for ATP hydrolysis, and the membrane-integral V₀ domain responsible for proton translocation. V-ATPase plays an essential role in energizing secondary active transport and is indispensable to plants. In addition to multiple stress responses, plant V-ATPase is also implicated in physiological processes such as growth, development, and morphogenesis. Based on the identification of distinct V-ATPase mutants and advances in luminal pH measurements in vivo, it has been revealed that this holoenzyme complex plays a pivotal role in pH homeostasis of the plant endomembrane system and endocytic and secretory trafficking. Here, we review recent progress in comprehending the biochemical properties and physiological functions of plant V-ATPase and explore the topics that require further elucidation.

Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture

Environmental stress is a major challenge for sustainable food production as it reduces yield by generating reactive oxygen species (ROS) which pose a threat to cell organelles and biomolecules such as proteins, DNA, enzymes, and others, leading to apoptosis. Plant growth-promoting rhizobacteria (PGPR) offers an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices in accomplishing sustainable agriculture by boosting growth and stress tolerance in plants. PGPR inhabit the rhizosphere of soil and exhibit positive interaction with plant roots. These organisms render multifaceted benefits to plants by several mechanisms such as the release of phytohormones, nitrogen fixation, solubilization of mineral phosphates, siderophore production for iron sequestration, protection against various pathogens, and stress. PGPR has the potential to curb the adverse effects of various stresses such as salinity, drought, heavy metals, floods, and other stresses on plants by inducing the production of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. Genetically engineered PGPR strains play significant roles to alleviate the abiotic stress to improve crop productivity. Thus, the present review will focus on the impact of PGPR on stress resistance, plant growth promotion, and induction of antioxidant systems in plants.

Comparative transcriptome analysis reveals the molecular mechanism of salt tolerance in Apocynum venetum

Apocynum venetum is a traditional Chinese medicinal herb with tolerance to various abiotic stresses, especially, salinity. However, only a few studies have investigated the salt-tolerant mechanism of this non-halophyte under salt stress at phenotypic and physiological levels. To explore the molecular mechanism of salinity tolerance in A. venetum, the global transcriptome profiles of seedling leaves under different salt-stress durations, using 200 mM NaCl, were analyzed. De novo assembly of approximately 715 million high-quality reads and approximately 105.61 Gb sequence data was performed. In total, 2822 differentially expressed genes (DEGs) were identified. DEGs were significantly enriched in flavonoid metabolism-related pathways such as "flavonoid biosynthesis" and "phenylpropanoid biosynthesis". Most of these DEGs were downregulated under salt stress. However, genes encoding the non-selective cation channels and antioxidants were upregulated under salt stress, whereas most cell wall-related DEGs were downregulated. Consequently, the concentration of flavonoids decreased, whereas that of Na⁺ increased with exposure time. Thus, we hypothesized that the accumulation of Na⁺ in the leaves, which resulted in reduced flavonoid concentration under salt stress, directly led to a decrease in the salt tolerance of A. venetum. This was verified by overexpressing four flavonoid synthesis pathway genes in Arabidopsis. The transgenic plants showed higher salt tolerance than the wild-type plants due to the accumulation of total flavonoids. These physiological and transcriptome analyses of A. venetum revealed major molecular underpinnings contributing to the responses of A. venetum to salt stress, thereby improving our understanding of the molecular mechanisms underlying salt tolerance in A. venetum and plants in general. The findings serve as a basis for functional studies on and engineering strategies for plant salinity tolerance.

Silicon biology in crops under abiotic stress: A paradigm shift and cross-talk between genomics and proteomics

Silicon is a beneficial element to improve the biological process, growth, development, and crop productivity. The review mainly focuses on the advantage of crops supplemented with silicon, how Si alleviate abiotic stress as well as regulate the genes and proteins involved in metabolic and biological functions in plants. Abiotic stress causes damage to the proteins, nucleic acids, affect transpiration rate, stomatal conductance, alter the nutrient balance, and cell desiccation which could reduce the growth and development of the plants. To overcome from this problem researchers, focus on beneficial element like silicon to protect the plants against various abiotic stresses. The previous review reports are based on the application of silicon on salinity and drought stress, plant defense mechanism, the elevation of plant metabolism, enhancement of the biochemical and physiological properties, regulation of secondary metabolites and plant hormone. Here, we discuss about the silicon uptake and accumulation in plants, and silicon regulates the reactive oxygen species under abiotic stress, further we mainly focus on the genes and proteins which play a vital role in plants with silicon supplementation. The study can help the researchers to focus further on plants to improve the advancement in them under abiotic stress.

The cytosolic invertase NI6 affects vegetative growth, flowering, fruit set, and yield in tomato

Sucrose metabolism is important for most plants, both as the main source of carbon and via signaling mechanisms that have been proposed for this molecule. A cleaving enzyme, invertase (INV) channels sucrose into sink metabolism. Although acid soluble and insoluble invertases have been largely investigated, studies on the role of neutral invertases (A/N-INV) have lagged behind. Here, we identified a tomato A/N-INV encoding gene (NI6) co-localizing with a previously reported quantitative trait locus (QTL) largely affecting primary carbon metabolism in tomato. Of the eight A/N-INV genes identified in the tomato genome, NI6 mRNA is present in all organs, but its expression was higher in sink tissues (mainly roots and fruits). A NI6-GFP fusion protein localized to the cytosol of mesophyll cells. Tomato NI6-silenced plants showed impaired growth phenotype, delayed flowering and a dramatic reduction in fruit set. Global gene expression and metabolite profile analyses of these plants revealed that NI6 is not only essential for sugar metabolism, but also plays a signaling role in stress adaptation. We also identified major hubs, whose expression patterns were greatly affected by NI6 silencing; these hubs were within the signaling cascade that coordinates carbohydrate metabolism with growth and development in tomato.

Improving ATPase and PPase activities, nutrient uptake and growth of salt stressed ajowan plants by salicylic acid and iron-oxide nanoparticles

Salicylic acid and iron-oxide nanoparticles alleviated salt toxicity and improved plant growth by stimulating the activities of H⁺-ATPase and H⁺-PPase and preventing nutrient imbalance. Two factorial experiments were undertaken in a greenhouse during 2018 and 2019, to evaluate the impacts of SA (1 mM) and nano-Fe₂O₃ (3 mM) sprays at 7 leaves and flowering stages on vacuolar H⁺-pumps, growth and essential oil of salt-subjected (0, 4, 8 and 12 dS m^-1 NaCl) ajowan plants. Measurements of plant traits were started at about 12 days after the last foliar spray and continued up to maturity. The H⁺-ATPase and H⁺-PPase activities and root ATP content were enhanced under low salinity, but higher salinities reduced these parameters. Rising salinity enhanced Na uptake and translocation, endogenous SA and DPPH activity, while reduced K⁺/Na⁺ ratio and nutrients uptake, leading to a reduction in plant biomass. Treatment with SA, nano-Fe₂O₃ and their combination improved H⁺-pumps activities and ATP content in roots and leaves. The SA-related treatments caused the highest activities of H⁺-pumps in roots, but Fe-related treatments resulted in the highest activities of these pumps in leaves. Increasing H⁺-pumps activities reduced sodium uptake and translocation and enhanced nutrients uptake. Foliar treatments, especially SA + nano-Fe₂O₃ augmented endogenous SA, DPPH activity, and plant growth in salt-stressed plants. Essential oil contents of vegetative and inflorescence organs under severe salinity and seeds under moderate and severe salinities were enhanced. Maximum essential oil was obtained from seeds of SA + nano-Fe₂O₃-treated plants, which was strongly correlated with endogenous SA and DPPH. Nevertheless, the SA + nano-Fe₂O₃ was the best treatment for diminishing salt toxicity and improving ajowan plant growth and essential oil production.

Comparative proteomic and transcriptomic analysis reveals high pH-induced expression signatures of Chinese shrimp Fenneropenaeus chinensis

pH has a great impact on the distribution, growth, behavior, and physiology in many aquatic animals. The comparison of proteomics between normal and high pH stress samples was successfully achieved using iTRAQ proteomic analysis to screen key response proteins and pathways. After high pH stress, 124 upregulated and 41 downregulated proteins were identified. The higher expression levels of proteins like citrate synthase, glutathione S-transferase, glutathione peroxidase, and cytochrome c oxidase are associated with oxidative stress and mitochondrial dysfunction. The upregulation of glucose-regulated protein 78 indicated that the endoplasmic reticulum stress is induced by high pH stress. There were significant upregulation expressions of V-type H⁺-ATPase, Na⁺, K⁺-ATPase, 14-3-3 protein, as well as ATP-binding cassette transmembrane transporters after high pH exposure, which indicating their important roles in response to high pH stress. The abundance of proteins involved in protein glycosylation, oxidative pentose phosphate pathway, protein export, and glutathione metabolism were found enriched in high pH group than in control group. Quantitative proteomic profiling and integrated analysis with transcriptomic data provide new insights into the mechanisms underlying the molecular response to high pH stress in Fenneropenaeus chinensis.

Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping

Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG(1-5).asl-5A, QG(1-5).asl-7B) sodium accumulation (QNa.asl-2A), chloride accumulation (QCl.asl-2A, QCl.asl-3A) and potassium:sodium ratio (QK:Na.asl-2DS2). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars.

Differential Morphophysiological and Biochemical Responses of Cotton Genotypes Under Various Salinity Stress Levels During Early Growth Stage

Cotton is a primary agriculture product important for fiber use in textiles and the second major oil seed crop. Cotton is considered as moderately tolerant to salt stress with salinity threshold of 7.7 dS/m at seedling stage. Salinity causes reduction in the growth of seedlings and cotton production that limits fiber quality and cotton yield. In this study, initially, 22 cotton genotypes were screened for relative salt tolerance using germination test in Petri plates (growth chamber). Selected 11 genotypes were further tested in pot experiment (sand) with 0, 15, and 20 dS/m NaCl treatments under glass house conditions. At four-leaves stage, different morphological and physiological traits were measured for all genotypes while biochemical analysis was performed on selected seven highly tolerant and sensitive genotypes. NaCl treatment significantly reduced plant biomass in two genotypes IR-NIBGE-13 and BS-2018, while NIAB-135, NIAB-512, and GH-HADI had least difference in fresh weight between the control and NaCl-treated plants. Photosynthetic rate was maintained in all the genotypes with the exception of SITARA-16. In two sensitive genotypes (IR-NIBGE-13 and 6071/16), Na⁺ ion accumulated more in leaves as compared to K⁺ ion under stress conditions, and an increase in Na⁺/K⁺ ratio was also observed. The lesser accumulation of malondialdehyde (MDA) content and higher activity of enzymatic antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX) in stressed plants of NIAB-135, NIAB-512, and FH-152 indicated that these genotypes had adaption capacity for salinity stress in comparison with sensitive genotypes, i.e., IR-NIBGE-13 and 6071/16. The observed salt tolerance was corelated with plant biomass maintenance (morphological), photosynthetic rate, and ionic homeostasis (K⁺/Na⁺ ratio, physiological) and biochemical stress marker regulations. After a series of experiments, it was concluded that NIAB-135, NIAB-512, and FH-152 could be utilized in breeding programs aimed at improving salinity tolerance in cotton and can expand cotton cultivation in saline area.

Ammonium Accumulation Caused by Reduced Tonoplast V-ATPase Activity in Arabidopsis thaliana

Plant vacuoles are unique compartments that play a critical role in plant growth and development. The vacuolar H⁺-ATPase (V-ATPase), together with the vacuolar H⁺-pyrophosphatase (V-PPase), generates the proton motive force that regulates multiple cell functions and impacts all aspects of plant life. We investigated the effect of V-ATPase activity in the vacuole on plant growth and development. We used an Arabidopsisthaliana (L.) Heynh. double mutant, vha-a2 vha-a3, which lacks two tonoplast-localized isoforms of the membrane-integral V-ATPase subunit VHA-a. The mutant is viable but exhibits impaired growth and leaf chlorosis. Nitrate assimilation led to excessive ammonium accumulation in the shoot and lower nitrogen uptake, which exacerbated growth retardation of vha-a2 vha-a3. Ion homeostasis was disturbed in plants with missing VHA-a2 and VHA-a3 genes, which might be related to limited growth. The reduced growth and excessive ammonium accumulation of the double mutant was alleviated by potassium supplementation. Our results demonstrate that plants lacking the two tonoplast-localized subunits of V-ATPase can be viable, although with defective growth caused by multiple factors, which can be alleviated by adding potassium. This study provided a new insight into the relationship between V-ATPase, growth, and ammonium accumulation, and revealed the role of potassium in mitigating ammonium toxicity.

Role of sulfur in combating arsenic stress through upregulation of important proteins, and in-silico analysis to study the interaction between phosphate transporter (PHO1), arsenic and phosphate in spinach

An adequate amount of Sulfur (S) is essential for proper plant growth and defence against abiotic stresses including metals and metalloids. Arsenic (As) contamination is increasing in agricultural soils rapidly due to anthropogenic activities. Sulfur deficiency and arsenic stress could be more harmful than these individual stresses alone. To understand the impact of S-deficiency and arsenic (31 ppm Na₃AsO₄ of soil) on ecophysiology, growth, inorganic phosphate level, and proteomic profile of spinach, the present study was conducted. Interaction of arsenic with phosphate transporters, phytochelatins, and glutathione was also analyzed in silico. Comparative 2D MS/MS proteomics helped in the identification of important proteins which might be the key players under S-deficiency and As stress. Upregulation and downregulation of 36 and 21 proteins under As stress; 19 and 36 proteins under S-deficiency; 38 and 31 proteins under combined stress, respectively was observed. A total, 87 proteins subjected to identification via MS/MS ion search were found to be associated with important plant functions. PHO1 abundance was highly influenced by As stress; hence an in-silico homology modeling based molecular docking was performed which indicated high interaction between PHO1 and As/phosphate. Varied proximity of arsenic with phosphate transporters, phytochelatin, and glutathione revealed these components as a potential target of As toxicity/detoxification in Spinach, reflecting sulfur as an important criterion for arsenic tolerance.

Vacuolar membrane H+-ATPase c`` subunit gene (ThVHAc``1) from Tamarix hispida Willd improves salt stress tolerance

The plant vacuolar H⁺-ATPase (V-ATPase) is a multisubunit complex. In addition to performing basic housekeeping functions, this complex is also involved in abiotic stress resistance in plants. In this study, a V-ATPase c`` subunit gene (ThVHAc``1) from Tamarix hispida Willd was cloned with a 534-bp ORF. Sequence analysis showed that the ThVHAc``1 protein contains four transmembrane helices and lacks a signal peptide. qRT-PCR results showed that ThVHAc``1 was primarily induced by treatments of NaCl, NaHCO₃, PEG₆₀₀₀, CdCl₂ or ABA in roots, stems and leaves of T. hispida. The expression pattern of ThVHAc``1 was significantly different from that of ThVHAc1 (a V-ATPase c subunit in T. hispida). Furthermore, the cell survival rates and density (OD<sub>600</sub>) results showed that the transgenic yeast overexpressing ThVHAc``1 exhibited increased tolerance to the above-mentioned abiotic stresses. In addition, the overexpression of ThVHAc``1 confers salt tolerance to transgenic Arabidopsis plants by improving the ROS content and decreasing the accumulation of O<sup>2-</sup> and H<sub>2</sub>O<sub>2</sub>. Similarly, the homologous transformation of the ThVHAc``1 gene into T. hispida also improved salt tolerance. Our results suggest that the ThVHAc``1 gene plays an important role in plant stress tolerance.

Monitoring the acclimatization of a Chlorella sp. From freshwater to hypersalinity using photosynthetic parameters of pulse amplitude modulated fluorometry

Contamination of freshwater raceway ponds impedes the commercial cultivation of microalgae. Acclimatization of freshwater microalgae to hypersaline conditions offers a means to reduce contamination. A freshwater Chlorella species was cultured in a gradient of salinities ranging from 5 to 40‰ and pulse amplitude modulated fluorometry recorded photosynthetic functioning. While the average salinity of seawater is 35‰, optimum acclimatization occurred at 20‰, at which point the growth rate (1.6 µg chl a L^-1d^-1) was not significantly different from the control (1.8 µg chl a L^-1d^-1). The maximum relative electron transfer rate was lower (9 to 12 µmol m^-2s^-1) at 5 to 20‰ as compared to 40‰ (28 µmol m^-2s^-1) where no algal growth was recorded. ATP and NADPH were thus shunted towards synthesis of molecules that offset cytoplasmic osmotic stress. Culturing this Chlorella strain in raceway ponds under saline conditions may reduce contamination and improve productivity.

A comparative proteomic analysis of engineered and bio synthesized silver nanoparticles on soybean seedlings

Nanoparticles (NPs) are synthesized by different methods and response mechanism of plants varied towards NPs based on their origin. To study the effects of bio synthesized (BS) and chemically synthesized (CS) silver NPs on soybean, a gel-free/ label-free proteomic technique was used. Length of root and hypocotyl was enhanced by BS compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to 1 and 50 ppm. A total of 190 and 173 differentially changed proteins were identified in BS and CS silver NPs treated soybean, respectively. Twenty proteins commonly changed between BS and CS silver NPs treated soybean. Differentially-changed proteins were associated with protein-degradation and stress according to functional categorization. From proteomics, abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs treated soybean. These results suggest that BS silver NPs enhanced the growth of soybean by regulating proteins related to protein-degradation and ATP contents, which are negatively affected by CS silver NPs. BIOLOGICAL SIGNIFICANCE: This study highlighted the response mechanism of soybean towards bio synthesized (BS) and chemically synthesized (CS) silver nanoparticles (NPs) using a gel-free/ label-free proteomics technique. Length of root and hypocotyl was enhanced by BS silver NPs compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to other concentrations. Differentially changed proteins were associated with protein degradation and stress. From the proteomics, the abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs compared to BS silver NPs treated soybean. These results suggest that the BS silver NPs enhanced the growth of soybean by regulating the proteins related to protein degradation and ATP contents, which are negatively affected by the CS silver NPs.

Engineering salinity tolerance in plants: progress and prospects

There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.

Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress

Abiotic stresses comprise all nonliving factors, such as soil salinity, drought, extreme temperatures, and metal toxicity, posing a serious threat to agriculture and affecting the plant production around the world. Peanut (Arachis hypogaea L.) is one of the most important crops for vegetable oil, proteins, minerals, and vitamins in the world. Therefore, it is of importance to understand the molecular mechanism of peanut against salt stress. Six transcriptome sequencing libraries including 24-hour salt treatments and control samples were constructed from the young leaves of peanut. A comprehensive analysis between two groups detected 3,425 differentially expressed genes (DEGs) including 2,013 upregulated genes and 1,412 downregulated genes. Of these DEGs, 141 transcription factors (TFs) mainly consisting of MYB, AP2/ERF, WRKY, bHLH, and HSF were identified in response to salinity stress. Further, GO categories of the DEGs highly related to regulation of cell growth, cell periphery, sustained external encapsulating structure, cell wall organization or biogenesis, antioxidant activity, and peroxidase activity were significantly enriched for upregulated DEGs. The function of downregulated DEGs was mainly enriched in regulation of metabolic processes, oxidoreductase activity, and catalytic activity. Fourteen DEGs with response to salt tolerance were validated by real-time PCR. Taken together, the identification of DEGs' response to salt tolerance of cultivated peanut will provide a solid foundation for improving salt-tolerant peanut genetic manipulation in the future.

Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress

Salinity represents a very limiting factor that affects the fertility of agricultural soils. Although grapevine is moderately susceptible to salinity, both natural causes and agricultural practices could worsen the impact of this abiotic stress. A promising possibility to reduce this problem in vineyards is the use of appropriate graft combinations. The responses of grapevine rootstocks to this abiotic stress at the root level still remain poorly investigated. In order to obtain further information on the multifaceted responses induced by salt stress at the biochemical level, in the present work we analyzed the changes that occurred under control and salt conditions in the root proteomes of two grapevine rootstock genotypes, M4 and 101.14. Moreover, we compared the results considering that M4 and 101.14 were previously described to have lower and higher susceptibility to salt stress, respectively. This study highlighted the greater capability of M4 to maintain and adapt energy metabolism (i.e., synthesis of ATP and NAD(P)H) and to sustain the activation of salt-protective mechanisms (i.e., Na sequestration into the vacuole and synthesis of osmoprotectant compounds). Comparitively, in 101.14 the energy metabolism was deeply affected and there was an evident induction of the enzymatic antioxidant system that occurred, pointing to a metabolic scenario typical of a suffering tissue. Overall, this study describes for the first time in grapevine roots some of the more crucial events that characterize positive (M4) or negative (101.14) responses evoked by salt stress conditions.

SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China

The Chinese elm is an important tree ecologically; however, little is known about its genetic diversity and adaptation mechanisms. In this study, a total of 107 individuals collected from seven natural populations in eastern China were investigated by specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) detected by SLAF-seq, genetic diversity and markers associated with climate variables were identified. All seven populations showed medium genetic diversity, with PIC values ranging from 0.2632 to 0.2761. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Environmental association analyses with three climate variables (annual rainfall, annual average temperature, and altitude) resulted in, altogether, 43 and 30 putative adaptive loci by Bayenv2 and LFMM, respectively. Five adaptive genes were annotated, which were related to the functions of glycosylation, peroxisome synthesis, nucleic acid metabolism, energy metabolism, and signaling. This study was the first on the genetic diversity and local adaptation in Chinese elms, and the results will be helpful in future work on molecular breeding.

Response of transgenic tobacco overexpressing the CchGLP gene to cadmium and aluminium: phenotypic and microRNAs expression changes

Transgenic tobacco (N. tabacum cv. Xanthi nc) expressing Capsicum chinense CchGLP gene that encodes an Mn-SOD, constitutively produces hydrogen peroxide that increase endogenous ROS levels. Previous studies using these plants against geminivirus infections as well as drought stress confirmed that CchGLP expression conferred resistance against biotic and abiotic stresses. Cadmium (Cd) and Aluminium (Al) contamination in soils are a major ecological concern since they are two of the most widespread toxic elements in terrestrial environments. Trying to explore additional possible tolerance to another stresses in these plants, the aim of this work was to analyse the response to cadmium and aluminium salts during germination and early stages of plantlet development and a differential transcriptome of microRNAs (miRNAs) expression in expressing CchGLP transgenic lines and an azygote non-CchGLP expressing line. Plants were grown in vitro with addition of CdCl₂ and AlCl₃ at three different concentrations: 100, 300 and 500 μM and 50, 150 and 300 μM, respectively. The results showed higher tolerance to Cd and Al salts evaluated in two CchGLP-expressing transgenic lines L8 and L26 in comparison with the azygous non-CchGLP expressing line L1. Interestingly, L8 under Al stress presented vigorous roots and development of radicular hairs in comparison with azygous control (L1). Differentially expressed miRNAs in the comparison between L8 and L1 were associated with up and down-regulation of target genes related with structural molecule activity and ribosome constituents, as well as down-regulation in proton-transporting V-type ATPase (Vacuolar ATPase or V-ATPase). Moreover, KEGG analysis of the target genes for the differentially expressed miRNAs, led to identification of genes related with metabolic pathways and biosynthesis of secondary metabolites. One possible explanation of the tolerance to Cd and Al displayed in the transgenic tobaccos evaluated, might involve the fact that several down-regulated miRNAs, were found associated with target genes expressing V-ATPase. Specifically, miR7904-5p was down regulated and related with the up-regulation of one V-ATPase. The expression levels of these genes was confirmed by qRT-PCR assays, thus suggesting that a cation transport activity driven by the V-ATPases-dependent proton motive force, might significantly contribute as one mechanism for Cd and Al detoxification by vacuolar compartmentation in these transgenic tobacco plants.

Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure

The conversion of light energy into chemical energy in leaves is very important for plant growth and development. During this process, chlorophylls and their derivatives are indispensable as their fundamental role in the energy absorption and transduction activities. Chlorophyll variation mutants are important materials for studying chlorophyll metabolism, chloroplast biogenesis, photosynthesis and related physiological processes. Here, a chlorophyll-reduced mutant (crm1) was isolated from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Compared to wild type, crm1 showed yellow leaves, reduced chlorophyll content, fewer thylakoid stacks and retarded growth. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 4575 proteins were identified from the chloroplast of Brassica napus leaves, and 466 of which displayed differential accumulations between wild type and crm1. The differential abundance proteins were found to be involved in chlorophyll metabolism, photosynthesis, phagosome and proteasome. Our results suggest that the decreased abundance of chlorophyll biosynthetic enzymes, proteins involved in photosynthesis might account for the reduced chlorophyll content, impaired thylakoid structure, and reduction of plant productivity. The increased abundance of proteins involved in phagosome and proteasome pathways might allow plants to adapt the proteome to environmental conditions to ensure growth and survival due to chlorophyll reduction. BIOLOGICAL SIGNIFICANCE: Photosynthesis, which consists of light and dark reactions, is fundamental to biomass production. Chloroplast is regarded as the main site for photosynthesis. During photosynthesis, the pigment chlorophyll is essential for light harvesting and energy transfer. This work provides new insights into protein expression patterns, and enables the identification of many attractive candidates for investigation of chlorophyll biosynthesis, chloroplast structure and photosynthesis in Brassica napus. These findings may be applied to improve the photosynthetic efficiency by genetic engineering in crops.

Expression of V-PPase proton pump, singly or in combination with a NHX1 transporter, in transgenic tobacco improves copper tolerance and accumulation

One of the most important strategies evolved by plants to tolerate heavy metals (HMs) is their sequestration into the vacuole. Recent studies have demonstrated that Cu sequestration into vacuole is dependent on the electrochemical gradient generated by vacuolar proton pumps: the V-H+-PPase and the V-H+-ATPase. In a previous study, we demonstrated that co-expression of V-H+-PPase and a sodium/proton antiporter genes, isolated from wheat, in transgenic tobacco plants significantly increases both H+ pumping activity of the endogenous V-H+-ATPase and V-H+-PPase compared to wild-type (WT) plants, all grown in the absence of stress. In the present study, we evaluated the effect of expression, in tobacco, of vacuolar proton pump, TaVP1, singly or in combination with sodium/proton antiporter, TaNHXS1, on copper (Cu) tolerance and accumulation. Results showed that, when subjected to Cu stress, TaVP1 single transgenic tobacco lines exhibited a more robust root system, greater biomass production, less chlorophyll loss, lower MDA and H2O2 production, and higher catalase activity and accumulated more Cu than did WT. Interestingly, double transgenic tobacco lines exhibited the best Cu tolerance and accumulation than either of the single TaVP1 transgenic lines or WT plants, when subjected to excess Cu. In fact, double transgenic lines accumulated 2.5-fold and 1.9-fold more Cu than did WT and single TaVP1 lines, respectively. Thus, these results clearly demonstrate the usefulness of expression of vacuolar proton pump alone or in combination with sodium/proton antiporter as novel strategy for Cu phytoremediation.

Functional analysis of McSnRK1 (SNF1-related protein kinase 1) in regulating Na/K homeostasis in transgenic cultured cells and roots of halophyte Mesembryanthemum crystallinum

Transgenic callus and roots of ice plant with altered SnRK1 function were established using Agrobacterium-mediated transformation. The role of McSnRK1 in controlling Na⁺ influx and Na/K ratio was demonstrated. SnRK1 kinases (SNF1-related protein kinase1) control metabolic adaptation during energy deprivation and regulate protective mechanisms against environmental stress. Yeast SNF1 activates a P-type ATPase, the Na⁺ exclusion pump, under glucose starvation. The involvement of plant SnRK1 in salt stress response is largely unknown. We previously identified a salt-induced McSnRK1 in the halophyte ice plant (Mesembryanthemum crystallinum). In the current study, the function of McSnRK1 in salt tolerance was analyzed in transgenic cultured cells and roots of ice plant. Ice plant callus constitutively expressed a high level of McSnRK1 and introducing the full-length McSnRK1 did not alter the Na/K ratio at 24 h after 200 mM NaCl treatment. However, interfering with McSnRK1 activity by introducing a truncate McSnRK1 to produce a dominant-negative form of McSnRK1 increased cellular Na⁺ accumulation and Na/K ratio. As a result, the growth of cultured cells diminished under salt treatment. Hydroponically grown ice plants with roots expressing full-length McSnRK1 had better growth and lowered Na/K ratio compared to the wild-type or vector-only plants. Roots expressing a truncate McSnRK1 had reduced growth and high Na/K ratio under 400 mM NaCl treatment. The changes in Na/K ratio in transgenic cells and whole plants demonstrated the function of SnRK1 in controlling Na⁺ flux and maintaining Na/K homeostasis under salinity. The Agrobacterium-mediated transformation system could be a versatile tool for functional analysis of genes involved in salt tolerance in the ice plant.

Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus

Environmental salinity is an important abiotic factor influencing normal physiological functions and productive performance in the sea cucumber Apostichopus japonicus. It is therefore important to understand how changes in salinity affect sea cucumbers in the face of global climate change. In this study, we investigated the responses to salinity stress in sea cucumbers using mRNA and miRNA sequencing. The regulatory network of mRNAs and miRNAs involved in salinity stress was examined, and the metabolic pathways enriched for differentially expressed miRNAs and target mRNAs were identified. The top 20 pathways were involved in carbohydrate metabolism, fatty acid metabolism, degradation, and elongation, amino acid metabolism, genetic information processing, metabolism of cofactors and vitamins, transport and catabolism, and environmental information processing. A total of 22 miRNAs showed differential expression during salinity acclimation. The predicted 134 target genes were enriched in functions consistent with the results of gene enrichment based on transcriptome analysis. These results suggested that sea cucumbers deal with salinity stress via changes in amino acid metabolism, ion channels, transporters, and aquaporins, under stimulation by environmental signals, and that this process requires energy from carbohydrate and fatty acid metabolism. Salinity challenge also induced miRNA expression. These results provide a valuable genomic resource that extends our understanding of the unique biological characteristics of this economically important species under conditions of salinity stress.

Balance between nitrogen use efficiency and cadmium tolerance in Brassica napus and Arabidopsis thaliana

The transmembrane transport of NO₃^- and Cd²⁺ into plant cell vacuoles relies on the energy from their tonoplast proton pumps, V-ATPase and V-PPase. If the activity of these pumps is reduced, it results in less NO₃^- and Cd²⁺ being transported into the vacuoles, which contributes to better nitrogen use efficiency (NUE) and lower Cd²⁺ tolerance in plants. The physiological mechanisms that regulate the balance between NUE and Cd²⁺ tolerance remain unknown. In our study, two Brassica napus genotypes with differential NUEs, xiangyou 15 and 814, and Atclca-2 mutant and AtCAX4 over-expression line (AtCAX4-OE) of Arabidopsis thaliana, were used to investigate Cd²⁺ stress responses. We found that the Brassica napus genotype, with higher NUE, was more sensitive to Cd²⁺ stress. The AtCAX4-OE mutant, with higher Cd²⁺ vacuolar sequestration capacity (VSC), limited NO₃^- sequestration into root vacuoles and promoted NUE. Atclca-2 mutants, with decreased NO₃^- VSC, enhanced Cd²⁺ sequestration into root vacuoles and conferred greater Cd²⁺ tolerance than the WT. This may be due to the competition between Cd²⁺ andNO₃^- in the vacuoles for the energy provided by V-ATPase and V-PPase. Regulating the balance between Cd²⁺ and NO₃^- vacuolar accumulation by inhibiting the activity of CLCa transporter and increasing the activity of CAX4 transporter will simultaneously enhance both the NUE and Cd²⁺ tolerance of Brassica napus, essential for improving its Cd²⁺ phytoremediation potential.

Interaction between the signaling molecules hydrogen sulfide and hydrogen peroxide and their role in vacuolar H+ -ATPase regulation in cadmium-stressed cucumber roots

Vacuolar H⁺ -ATPase (V-ATPase; EC 3.6.3.14) is the main enzyme responsible for generating a proton gradient across the tonoplast. Under cadmium (Cd) stress conditions, V-ATPase activity is inhibited. In the present work, hydrogen sulfide (H₂ S) and hydrogen peroxide (H₂ O₂ ) cross-talk was analyzed in cucumber (Cucumis sativus L.) seedlings exposed to Cd to explain the role of both signaling molecules in the control of V-ATPase. V-ATPase activity and gene expression as well as H₂ S and H₂ O₂ content and endogenous production were determined in roots of plants treated with 100 μM CdCl₂ and different inhibitors or scavengers. It was found that H₂ S donor improved photosynthetic parameters in Cd-stressed cucumber seedlings. Cd-induced stimulation of H₂ S level was correlated with the increased activities of the H₂ S-generating desulfhydrases. Increased H₂ O₂ and lowered H₂ S contents in roots were able to reduce V-ATPase activities similar to Cd. H₂ O₂ and H₂ S-induced modulations in V-ATPase activities were not closely related to the transcript level of encoding genes, suggesting posttranslational modifications of enzyme protein. On the other hand, exogenous H₂ O₂ raised H₂ S content in root tissues independently from the desulfhydrase activity. Although treatment of control plants with H₂ S significantly stimulated NADPH oxidase activity and gene expression, H₂ S did not affect H₂ O₂ accumulation in roots exposed to Cd. The results suggest the existence of two pathways of H₂ S generation in Cd-stressed cucumber roots. One involves desulfhydrase activity, as was previously demonstrated in different plant species. The other, the desulfhydrase-independent pathway induced by H₂ O₂ /NADPH oxidase, may protect V-ATPase from inhibition by Cd.

Comparative proteomics analysis of peanut roots reveals differential mechanisms of cadmium detoxification and translocation between two cultivars differing in cadmium accumulation

BACKGROUND

Peanut is one of the most important oil and protein crops, and it exhibits wide cultivar variations in shoot Cd accumulation ability. However, the mechanism of Cd accumulation in peanut shoots has not been well understood. In this study, the root proteomics of two cultivars differing in seed Cd accumulation, Fenghua 1 (F, low Cd cultivar) and Silihong (S, high Cd cultivar), were investigated under 0 (CK) and 2 μM Cd conditions.

RESULTS

A total of 4676 proteins were identified by proteomics screening. Of them, 375, 1762, 1276 and 771 proteins were identified to be differentially expressed proteins (DEPs) for comparison of F_Cd/F_CK, S_Cd/S_CK, F_CK/S_CK and F_Cd/S_Cd, respectively. Silihong is more sensitive to Cd exposure than Fenghua 1 in terms of root proteomics. A total of 30 and 86 DEPs were identified to be related with heavy metal transport and cell wall modification, respectively. The up-regulation of ABCB25, ABCC14, ABCC2, PDR1 and V-ATPases by Cd exposure in Silihong might enhance vacuolar sequestration of Cd and its efflux from symplast to apoplast. The higher Cd accumulation in the root CWs of Silihong might be resulted from its higher capability of CW modification, in which many proteins such as IRX10L, BGLU12-like, BGLU42, EXLB1, XTH30, XTH6, XYL7, PAL3, COMT, CAD1, and CCR1 were involved.

CONCLUSIONS

The vacuolar sequestration and efflux of Cd as well as its adsorption in CW might be the principal mechanism of cadmium detoxification in Silihong. The higher capacity of Cd accumulation and translocation of Silihong is an inherent characteristics in which ACA8 and ZIP1 might be involved.

Comparative proteomic analysis of salt-responsive proteins in canola roots by 2-DE and MALDI-TOF MS

Salinity stress is a major abiotic stress that affects plant growth and limits crop production. Roots are the primary site of salinity perception, and salt sensitivity in roots limits the productivity of the entire plant. To better understand salt stress responses in canola, we performed a comparative proteomic analysis of roots from the salt-tolerant genotype Safi-7 and the salt-sensitive genotype Zafar. Plants were exposed to 0, 150, and 300 mM NaCl. Our physiological and morphological observations confirmed that Safi-7 was more salt-tolerant than Zafar. The root proteins were separated by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry was applied to identify proteins regulated in response to salt stress. We identified 36 and 25 protein spots whose abundance was significantly affected by salt stress in roots of plants from the tolerant and susceptible genotype, respectively. Functional classification analysis revealed that the differentially expressed proteins from the tolerant genotype could be assigned to 14 functional categories, while those from the susceptible genotype could be classified into 9 functional categories. The most significant differences concerned proteins involved in glycolysis (Glyceraldehyde-3-phosphate dehydrogenase, Fructose-bisphosphate aldolase, Phosphoglycerate kinase 3), stress (heat shock proteins), Redox regulation (Glutathione S-transferase DHAR1, L-ascorbate peroxidase), energy metabolism (ATP synthase subunit B), and transport (V-type proton ATPase subunit B1) which were increased only in the tolerant line under salt stress. Our results provide the basis for further elucidating the molecular mechanisms of salt-tolerance and will be helpful for breeding salt-tolerant canola cultivars.

Differential response of Indian mustard (Brassica juncea L., Czern and Coss) under salinity: photosynthetic traits and gene expression

To explore the effect of salt stress on photosynthetic traits and gene expression in Indian mustard, four genotypes CS 54 (national check for salinity), CS 52-SPS-1-2012 (salt tolerant mutant), CS 614-4-1-4-100-13 (salt sensitive mutant) and Pusa bold (high yielding variety) were evaluated under irrigation water salinity (ECiw 12, and 15 dS m-1). Results suggest genotype CS 52-SPS-1-2012 followed by CS 54 performed better under imposed salt stress due to differential regulation of Na+ accumulation in the roots and main stem, restriction of Na+ influx from root to shoot, maintaining higher net photosynthetic traits under saline stress compared to CS 614-4-1-4-100-13 and Pusa bold. Further, overexpression of antiporters (SOS1, SOS2, SOS3, ENH1 and NHX1) and antioxidant (APX1, APX4, DHAR1 and MDHAR) genes in salt tolerant genotypes CS 52-SPS-1-2012 and CS 54 demonstrated their significant role in imparting salt tolerance in Indian mustard.

Differences in Root Physiological and Proteomic Responses to Dibutyl Phthalate Exposure between Low- and High-DBP-Accumulation Cultivars of Brassica parachinensis

Di- n-butyl phthalate (DBP), as an endocrine-disrupting chemical that tends to be accumulated in crops, poses great risks to human health through the food chain. To identify the molecular mechanism underlying differences in their DBP accumulation, the root physiological and proteomic responses to DBP stress of two Brassica parachinensis cultivars, a high-DBP accumulator (Huaguan) and a low-DBP accumulator (Lvbao), were investigated. Root damage of greater severity and significantly greater ( p < 0.05) decreases in root protein content and root activity were detected in Lvbao than in Huaguan, suggesting that Lvbao had lower tolerance to DBP. In total, 52 DBP-responsive proteins were identified by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. More proteins involved in basic metabolic processes, such as protein synthesis and energy metabolism, were downregulated in Lvbao, possibly explaining its lower tolerance and root damage. Several proteins involved in starch metabolism, cell-wall biosynthesis and modification, and stress response were activated in Huaguan, suggesting greater tolerance to DBP. Overall, differences in root proteome between the two cultivars might be responsible for the genotype-dependent DBP tolerance and accumulation in B. parachinensis.

Proteomic and ecophysiological responses of soybean (Glycine max L.) root nodules to Pb and hg stress

BACKGROUND

Lead (Pb) and mercury (Hg) are persistent hazardous metals in industrially polluted soils which can be toxic in low quantities. Metal toxicity can cause changes at cellular and molecular level which should be studied for better understanding of tolerance mechanism in plants. Soybean (Glycine max L.) is an important oilseed crop of the world including India. Indian soils growing soybean are often contaminated by Pb and Hg. The aim of this study was to explore how soybean root nodule responds to Pb and Hg through proteomic and ecophysiological alterations in order to enhance tolerance to metal stress.

RESULTS

Soybean plants were exposed to Pb (30 ppm PbCl2) and Hg (0.5 ppm HgCl2) to study histological, histochemical, biochemical and molecular response of N2-fixing symbiotic nodules. Both Pb and Hg treatment increased the level of oxidative stress in leaves and nodules. Chlorosis in leaves and morphological/anatomical changes in nodules were observed. Activities of ascorbate peroxidase, glutathione reductase and catalase were also modulated. Significant changes were observed in abundance of 76 proteins by Pb and Hg. Pb and Hg influenced abundance of 33 proteins (17 up and 16 down) and 43 proteins (33 up and 10 down), respectively. MS/MS ion search identified 55 proteins which were functionally associated with numerous cellular functions. Six crucial proteins namely catalase (CAT), allene oxide synthase (AOS), glutathione S-transferase (GST), calcineurin B like (CBL), calmodulin like (CML) and rapid alkalinisation factor (RAF) were selected for transcript abundance estimation. The qRT-PCR based real time expression exhibited a positive correlation with proteomics expression except for GST and RAF.

CONCLUSION

Soybean root nodule responds to metal stress by increased abundance of defence, development and repair related proteins. An efficient proteomic modulation might lead to metal-induced stress tolerance in N2-fixing nodules. Although concentrations of Pb and Hg used in the study cannot be considered equimolar, yet Hg seems to induce more changes in nodule proteomic profile, and higher damage to both bacteroides and root anatomy.