Abscisic acid pretreatment enhances salt tolerance of rice seedlings: proteomic evidence

Effects of foliar spraying with melatonin and chitosan Nano-encapsulated melatonin on tomato (Lycopersicon esculentum L. cv. Falcato) plants under salinity stress

Melatonin has been found to be crucial in the growth and development of plants under stress conditions. In this study, the effects of melatonin and nano melatonin regarding the growth and development of tomato plants, along with their photosynthetic pigment, phenol, and antioxidant activity, were investigated under saline conditions. The study was conducted using a completely randomized design with three replications, and the applied treatments were salt stress and foliar spraying of melatonin at a concentration of 0 (control), melatonin (Mel), and nano capsule-melatonin (Nano-Mel) at 500 µM. Salinity treatments included application of sodium chloride with two concentration of 0 mM NaCl (S1) and 50 mM NaCl (S2). Under saline conditions, Mel and Nano-Mel increased both shoot and root fresh and dry weights, improved relative water content (RWC), and enhanced antioxidant activity and phenolic content. Salinity elevated leaf ABA content, unaffected by Mel or Nano-Mel. Chlorophyll fluorescence and SPAD values demonstrated resilience to salinity with Mel and Nano-Mel applications. Nano-Mel notably mitigated Na + accumulation in leaves under salinity, helping maintain K + homeostasis. Proline levels rise due to salinity but decreased with Mel and Nano-Mel treatments. Electrolyte leakage (EL) increased under salinity but is significantly reduced by Mel, indicating enhanced membrane stability. The findings reveal that salinity stress significantly reduced plasma membrane intrinsic protein (PIP) expression in roots and leaves, whereas Mel and Nano-Mel treatments enhance PIP expression, particularly in roots. The study concludes that Mel and Nano-Mel effectively alleviate salinity-induced stress, promoting growth and maintaining physiological homeostasis in tomato plants.

Exogenous ABA promotes resistance to Sitobion avenae (Fabricius) in rice seedlings

BACKGROUND

Over the course of evolution, plants have developed various sophisticated defense mechanisms to resist pests and diseases. The phytohormone abscisic acid (ABA) has an important role in the growth and development of plants and confers tolerance to selected abiotic stressors, such as drought. Previous studies have shown that ABA promotes the deposit of callose in response to piercing/sucking insect pests. The English grain aphid, Sitobion avenae Fabricius, causes huge losses in rice and is especially harmful to rice seedlings.

RESULTS

Exogenous ABA promoted growth and reduced the feeding behavior of S. avenae nymphs in rice. Our results suggested that enhanced trichome density and increased expression of related genes may be associated with rice resistance to aphids. An analysis of volatiles revealed the production of seven compounds associated with pest resistance.

CONCLUSION

These results indicate that ABA reduces aphid feeding in rice. Our findings provide a basis for understanding ABA-mediated defense responses in rice and provide insights on more environmentally-friendly approaches to control. © 2024 Society of Chemical Industry.

Effect of drought stress on the expression pattern of genes involved in ABA biosynthesis in Desi-type chickpea (Cicer arietinum L.)

BACKGROUND

The behavior of Abscisic acid (ABA) as a stress phytohormone may be involved in mechanisms leading to tolerance and survival in adverse environmental conditions such as drought stress.

METHODS

Here, we evaluated ABA-mediated responses at physio-biochemical and molecular levels in drought-stressed seedlings of two different Desi-type chickpea genotypes (10 as a tolerant genotype and 247 as a sensitive one).

RESULTS

Under drought stress, two chickpea genotypes showed a decrease in their relative water content (RWC), and the intense decrease was related to the sensitive genotype (73.9%) in severe stress. Hydrogen peroxide (H2O2) and malondialdehyde (MDA) concomitant with the severity of stress increased in genotypes and the higher increase was in the sensitive genotype (5.8-fold and 3.43-fold, respectively). In the tolerant genotype, the enhanced accumulation of total phenolic content (1.75-fold) and radical scavenging action, based on 1,1-diphenyl-2-picrylhydrazyl test (DPPH), (1.69-fold) were simultaneous with ABA accumulation (1.53-fold). In the tolerant genotype, transcriptional analysis presented upregulation of Zeaxanthin epoxidase (ZEP) (1.35-fold), 9-cis-epoxycarotenoid dioxygenase (NCED) (5.16-fold), and Abscisic aldehyde oxidase (AAO) (1.52-fold compared to control conditions) genes in severe stress in comparison with mild stress. The sensitive genotype had a declining trend in total chlorophyll (up to 70%) and carotenoid contents (36%). The main conclusion to be drawn from this investigation is that ABA with its regulatory effects can affect drought tolerance mechanisms to alleviate adverse effects of unsatisfactory environmental conditions.

CONCLUSIONS

In this paper, we tried to indicate that drought stress induces overexpression of genes triggering ABA-mediated drought responses simultaneously in two genotypes while more increment expression was related to the tolerant genotype. At first thought, it seems that the tolerant genotype compared to the sensitive genotype has a genetically inherent ability to cope with and drop adverse effects of drought stress through over-accumulation of ABA as drought.

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

Caffeic acid O-methyltransferase (COMT) participates in various physiological activities in plants, such as positive responses to abiotic stresses and the signal transduction of phytohormones. In this study, 18 COMT genes were identified in the chromosome-level reference genome of mango, named MiCOMTs. A phylogenetic tree containing nine groups (I-IX) was constructed based on the amino acid sequences of the 71 COMT proteins from seven species. The phylogenetic tree indicated that the members of the MiCOMTs could be divided into four groups. Quantitative real-time PCR showed that all MiCOMT genes have particularly high expression levels during flowering. The expression levels of MiCOMTs were different under abiotic and biotic stresses, including salt and stimulated drought stresses, ABA and SA treatment, as well as Xanthomonas campestris pv. mangiferaeindicae and Colletotrichum gloeosporioides infection, respectively. Among them, the expression level of MiCOMT1 was significantly up-regulated at 6-72 h after salt and stimulated drought stresses. The results of gene function analysis via the transient overexpression of the MiCOMT1 gene in Nicotiana benthamiana showed that the MiCOMT1 gene can promote the accumulation of ABA and MeJA, and improve the salt tolerance of mango. These results are beneficial to future researchers aiming to understand the biological functions and molecular mechanisms of MiCOMT genes.

Mechanism of [CO2] Enrichment Alleviated Drought Stress in the Roots of Cucumber Seedlings Revealed via Proteomic and Biochemical Analysis

Cucumber is one of the most widely cultivated greenhouse vegetables, and its quality and yield are threatened by drought stress. Studies have shown that carbon dioxide concentration ([CO₂]) enrichment can alleviate drought stress in cucumber seedlings; however the mechanism of this [CO₂] enrichment effect on root drought stress is not clear. In this study, the effects of different drought stresses (simulated with 0, 5% and 10% PEG 6000, i.e., no, moderate, and severe drought stress) and [CO₂] (400 μmol·mol^-1 and 800 ± 40 μmol·mol^-1) on the cucumber seedling root proteome were analyzed using the tandem mass tag (TMT) quantitative proteomics method. The results showed that after [CO₂] enrichment, 346 differentially accumulating proteins (DAPs) were found only under moderate drought stress, 27 DAPs only under severe drought stress, and 34 DAPs under both moderate and severe drought stress. [CO₂] enrichment promoted energy metabolism, amino acid metabolism, and secondary metabolism, induced the expression of proteins related to root cell wall and cytoskeleton metabolism, effectively maintained the balance of protein processing and degradation, and enhanced the cell wall regulation ability. However, the extent to which [CO₂] enrichment alleviated drought stress in cucumber seedling roots was limited under severe drought stress, which may be due to excessive damage to the seedlings.

Exogenous melatonin enhances cell wall response to salt stress in common bean (Phaseolus vulgaris) and the development of the associated predictive molecular markers

Common bean (Phaseolus vulgaris) is an important food crop; however, its production is affected by salt stress. Salt stress can inhibit seed germination, promote senescence, and modify cell wall biosynthesis, assembly, and architecture. Melatonin, an indole heterocycle, has been demonstrated to greatly impact cell wall structure, composition, and regulation in plants under stress. However, the molecular basis for such assumptions is still unclear. In this study, a common bean variety, "Naihua" was treated with water (W), 70 mmol/L NaCl solution (S), and 100 μmol/L melatonin supplemented with salt solution (M+S) to determine the response of common bean to exogenous melatonin and explore regulatory mechanism of melatonin against salt stress. The results showed that exogenous melatonin treatment alleviated salt stress-induced growth inhibition of the common bean by increasing the length, surface area, volume, and diameter of common bean sprouts. Moreover, RNA sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) indicated that the cell wall regulation pathway was involved in the salt stress tolerance of the common bean enhanced by melatonin. Screening of 120 germplasm resources revealed that melatonin treatment improved the salt tolerance of more than 65% of the common bean germplasm materials. Melatonin also up-regulated cell wall pathway genes by at least 46%. Furthermore, we analyzed the response of the common bean germplasm materials to melatonin treatment under salt stress using the key genes associated with the synthesis of the common bean cell wall as the molecular markers. The results showed that two pairs of markers were significantly associated with melatonin, and these could be used as candidate markers to predict whether common bean respond to exogenous melatonin and then enhance salt tolerance at the sprouting stage. This study shows that cell wall can respond to exogenous melatonin and enhance the salt tolerance of common bean. The makers identified in this study can be used to select common bean varieties that can respond to melatonin under stress. Overall, the study found that cell wall could response melatonin and enhance the salt tolerance and developed the makers for predicting varieties fit for melatonin under stress in common bean, which may be applied in the selection or development of common bean varieties with abiotic stress tolerance.

Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return

Straw return is crucial for the sustainable development of rice planting, but no consistent results were observed for the effect of straw return on rice growth. To investigate the response of rice leaves to rice straw return in Northeast China, two treatments were set, no straw return (S0) and rice straw return (SR). We analyzed the physiological index of rice leaves and measured differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with the S0 treatment, the SR treatment significantly decreased the dry weight of rice plants and non-structural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves of SR treatment, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs were mainly involved in photosynthesis and oxidative phosphorylation, and DEMs were mainly involved in alpha-linolenic acid metabolism, galactose metabolism, glycerophospholipid metabolism, pentose and gluconic acid metabolism, and other metabolic pathways. Rice straw return promoted the accumulation of scavenging substances of active oxygen and osmotic adjustment substances, such as glutathione, organic acids, amino acids, and other substances. The SR treatment reduced the photosynthetic capacity and energy production of carbon metabolism, inhibiting the growth of rice plants, while the increase of metabolites involved in defense against abiotic stress enhanced the adaptability of rice plants to straw return stress.

Effects of Phloem-Feeding Pest, Dalbulus maidis on Morphological Expression of Drought-Tolerant Traits in Maize

Drought is amongst the most important stressors affecting maize production globally. Existing strategies to offset drought impacts are centered around the rapid development of drought-tolerant cultivars through plant breeding. However, under both current conditions and projected climate changes, additional stressors such as insect pests will co-occur. To determine the impact of combined insect and drought stress on drought tolerance in maize, we assessed the effects of Dalbulus maidis, drought, and both stresses combined in drought-tolerant maize hybrids. We measured several maize morphological growth traits (i.e., plant height, stem diameter, shoot weight, root weight, root length, and root-to-shoot ratio) at the end of a 28-day period of pulse-stress and no-stress control exposure. We found that seedling growth declined when both stressors co-occurred. Nevertheless, drought-tolerant maize hybrids remained strongly tolerant to drought regardless of D. maidis infestation. While our results showed that drought tolerance is maintained in drought-tolerant maize seedlings, future studies should address any effects on maize yield. Our study highlights the importance of testing the combined effects of drought and insect stressors to better predict insect–plant interactions in the context of plant breeding for drought-tolerant traits in a changing climate.

Effects of Melatonin Priming on Suaeda corniculata Seed Germination, Antioxidant Defense, and Reserve Mobilization: Implications for Salinized Wetland Restoration

Melatonin priming has been widely reported to positively affect seed germination under abiotic stresses. However, there is still a gap in knowledge on how melatonin priming impacts the seed germination and physiological change of wetland plant species. We assessed the effects of different melatonin concentrations on germination characteristics, antioxidant defense, and reserve mobilization of Suaeda corniculata seeds. Priming of S. corniculata seeds with 50 μM melatonin significantly improved the germination rate, germination speed, germination index, superoxide dismutase and peroxidase activity, and soluble sugar content as compared with the control, and effectively reduced the malondialdehyde content, promoted starch, soluble protein, and fat mobilization. However, the stress tolerance ability of S. corniculata seeds was reduced by high melatonin concentration. The structural equation model indicated that the melatonin priming directly affects the seed germination, while also indirectly regulating the antioxidant defense system and reserve mobilization. In conclusion, melatonin priming affects the S. corniculata seed germination under salinization stress in a concentration-dependent manner via both direct and indirect regulatory pathways. Insights into these aspects will advance our understanding of how melatonin priming affects S. corniculata seed germination and provide invaluable information and technical support for the restoration of salinized wetlands in the Momoge National Nature Reserve.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Mulching impact of Jatropha curcas L. leaves on soil fertility and yield of wheat under water stress

In present studies we have evaluated mulching impact of Jatropha curcas leaves on soil health and yield of two wheat (Triticum aestivum L.) varieties Wadan-2017 (rainfed) and Pirsabak-2013 (irrigated) under imposed water stress. Mulch of Jatropha leaves was spread on the soil surface at the rate of 0, 1, 3 and 5 Mg ha^-1 after seed germination of wheat. Water stress was imposed by skipping irrigations for one month at anthesis stage of wheat maintaining 40% soil field capacity. We found a significant decline in soil microbial biomass carbon (30.27%), total nitrogen (22.28%) and organic matter content (21.73%) due to imposed water stress in non-mulch plots. However, mulch application at 5 Mg ha^-1 significantly improved soil organic matter (38.18%), total nitrogen (37.75%), phenolics content (16.95 mg gallic acid equivalents/g) and soil microbial biomass carbon (26.66%) as compared to non-mulch control. Soil health indicators like soil carbonates, bicarbonates, electrical conductivity, chloride ions and total dissolved salts were decreased by 5 Mg ha^-1 mulch application. We noted a decline in yield indicators like spike weight (14.74%), grain spike^-1 (7.02%), grain length (3.79%), grain width (3.16%), 1000 grains weight (6.10%), Awn length (9.21%), straw weight (23.53%) and total grain yield (5.98%) of wheat due to imposed water stress. Reduction in yield traits of wheat due to water stress was higher in Pirsabak-2013 than Wadan-2017. Jatropha leaves mulch application at 5 Mg ha^-1 significantly minimized the loss in yield traits of wheat crop caused by water stress. Jatropha curcas leaves mulch application at 5 Mg ha^-1 is recommended for the successful establishment of wheat crop under water deficit conditions.

How salt stress-responsive proteins regulate plant adaptation to saline conditions

An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.

Exogenous phytohormones in the regulation of growth and development of cereals under abiotic stresses

Abiotic stresses, among which extreme temperatures, salinity, drought, UV radiation, heavy metal pollution, etc., adversely affect the growth and yield of cereals, the most important group of monocotyledonous plants that have met the nutritional and other needs of mankind for thousands of years. To cope with stress, plants deploy certain adaptive strategies that combine morphological, physiological, and biochemical responses, and on which growth and productivity depend. An important place in the formation of such strategies is occupied by phytohormones - signaling biomolecules of a different chemical structure and physicochemical properties, which act in nanomolar concentrations and regulate most physiological and metabolic processes of plants. In this review, the latest literature data concerning the growth and development regulation by exogenous phytohormones in cereals under abiotic stresses have been analyzed and summarized. The effects of priming and foliar treatment with abscisic acid, gibberellins, auxins, cytokinins, brassinosteroids, jasmonic and salicylic acids on the cultivated cereals tolerance to different abiotic stressors are discussed. Peculiarities of bilateral and multilateral hormonal signaling in the formation of responses of cultivated cereals to abiotic stressors after application of exogenous phytohormones are considered. The issue of exogenous phytohormones effects on molecular mechanisms controlling the synthesis of endogenous hormones, their signaling and activity are singled out. It is emphasized that phytohormonal engineering opens new opportunities to increase yields and is seen as an important promising approach to overcoming the cereal losses caused by adverse external factors.

Flooding or drought which one is more offensive on pepper physiology and growth?

Both extreme usage of water in agriculture i.e., drought and flooding affect physiological and growth aspects of the plant as well as gene expression undertaken in water absorption. These affect depend on the stress duration i.e., shock or gradual stress exposer. The factorial experiment based on CRD with 10 replicates was conducted to investigate the physiological and water relation as well as aquaporin expression in (Capsicum annuum L.). Drought stress was applied gradually from - 2, - 3, - 4 to - 5 MPa during 8 days but in shock stress - 5 MPa applied at one time. The gradual flooding stress adjusted with changing the aeration duration from 15 to 0 min gradually every 2 days and for the shock- flooding, peppers keep in a nutrient solution without aeration in a sealed container. Results showed that both extreme water stress had a deleterious effect on the growth and physiological parameter of pepper for a longer duration. Antioxidant, proline, fluorescence chlorophyll stimulate in the gradual period except for ABA content, which is higher in shock stress. PIP1expression showed a reverse effect in leaf and root at flooding i.e., PIP1expression raised in root while it was reduced in leaf at shock-flooding. The highest PIP1expression was observed in gradual-drought of root and gradual duration of drought and flooding stress in leaf. In the physiological aspect of plant response to stress in pepper, results showed an enhanced in proline and phenol content to help osmotic adjustment and keep water status in moderate condition. Conclusively, shocked stress first, motivated these defense systems, and then in the next step, the other adaptive mechanism like gene expression activated to help pepper face stress. On the other hand, shock stress showed down-regulation, but when the stress lasted for a longer time results in up-regulation.

Rhizospheric Bacillus spp. Rescues Plant Growth Under Salinity Stress via Regulating Gene Expression, Endogenous Hormones, and Antioxidant System of Oryza sativa L

Salinity has drastically reduced crop yields and harmed the global agricultural industry. We isolated 55 bacterial strains from plants inhabiting the coastal sand dunes of Pohang, Korea. A screening bioassay showed that 14 of the bacterial isolates secreted indole-3-acetic acid (IAA), 12 isolates were capable of exopolysaccharide (EPS) production and phosphate solubilization, and 10 isolates secreted siderophores. Based on our preliminary screening, 11 bacterial isolates were tested for salinity tolerance on Luria-Bertani (LB) media supplemented with 0, 50, 100, and 150 mM of NaCl. Three bacterial isolates, ALT11, ALT12, and ALT30, had the best tolerance against elevated NaCl levels and were selected for further study. Inoculation of the selected bacterial isolates significantly enhanced rice growth attributes, viz., shoot length (22.8-42.2%), root length (28.18-59%), fresh biomass (44.7-66.41%), dry biomass (85-90%), chlorophyll content (18.30-36.15%), Chl a (29.02-60.87%), Chl b (30.86-64.51%), and carotenoid content (26.86-70%), under elevated salt stress of 70 and 140 mM. Furthermore, a decrease in the endogenous abscisic acid (ABA) content (27.9-23%) and endogenous salicylic acid (SA) levels (11.70-69.19%) was observed in inoculated plants. Antioxidant analysis revealed an increase in total protein (TP) levels (42.57-68.26%), whereas it revealed a decrease in polyphenol peroxidase (PPO) (24.63-34.57%), glutathione (GSH) (25.53-24.91%), SOA (13.88-18.67%), and LPO levels (15.96-26.06%) of bacterial-inoculated plants. Moreover, an increase in catalase (CAT) (26-33.04%), peroxidase (POD) (59.55-78%), superoxide dismutase (SOD) (13.58-27.77%), and ascorbic peroxidase (APX) (5.76-22.74%) activity was observed. Additionally, inductively coupled plasma mass spectrometry (ICP-MS) analysis showed a decline in Na⁺ content (24.11 and 30.60%) and an increase in K⁺ (23.14 and 15.45%) and Mg⁺ (2.82 and 18.74%) under elevated salt stress. OsNHX1 gene expression was downregulated (0.3 and 4.1-folds), whereas the gene expression of OsPIN1A, OsCATA, and OsAPX1 was upregulated by a 7-17-fold in bacterial-inoculated rice plants. It was concluded that the selected bacterial isolates, ALT11, ALT12, and ALT30, mitigated the adverse effects of salt stress on rice growth and can be used as climate smart agricultural tools in ecofriendly agricultural practices.

Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress

Low-temperature stress is a type of abiotic stress that limits plant growth and production in both subtropical and tropical climate conditions. In the current study, the effects of 24-epi-brassinolide (EBR) as analogs of brassinosteroids (BRs) were investigated, in terms of hormone content, antioxidant enzyme activity, and transcription of several cold-responsive genes, under low-temperature stress (9 °C) in two different tomato species (cold-sensitive and cold-tolerant species). Results indicated that the treatment with exogenous EBR increases the content of gibberellic acid (GA3) and indole-3-acetic acid (IAA), whose accumulation is reduced by low temperatures in cold-sensitive species. Furthermore, the combination or contribution of BR and abscisic acid (ABA) as a synergetic interaction was recognized between BR and ABA in response to low temperatures. The content of malondialdehyde (MDA) and proline was significantly increased in both species, in response to low-temperature stress; however, EBR treatment did not affect the MDA and proline content. Moreover, in the present study, the effect of EBR application was different in the tomato species under low-temperature stress, which increased the catalase (CAT) activity in the cold-tolerant species and increased the glutathione peroxidase (GPX) activity in the cold-sensitive species. Furthermore, expression levels of cold-responsive genes were influenced by low-temperature stress and EBR treatment. Overall, our findings revealed that a low temperature causes oxidative stress while EBR treatment may decrease the reactive oxygen species (ROS) damage into increasing antioxidant enzymes, and improve the growth rate of the tomato by affecting auxin and gibberellin content. This study provides insight into the mechanism by which BRs regulate stress-dependent processes in tomatoes, and provides a theoretical basis for promoting cold resistance of the tomato.

Loss of COMT activity reduces lateral root formation and alters the response to water limitation in sorghum brown midrib (bmr) 12 mutant

Lignin is a key target for modifying lignocellulosic biomass for efficient biofuel production. Brown midrib 12 (bmr12) encodes the sorghum caffeic acid O-methyltransferase (COMT) and is one of the key enzymes in monolignol biosynthesis. Loss of function mutations in COMT reduces syringyl (S) lignin subunits and improves biofuel conversion rate. Although lignin plays an important role in maintaining cell wall integrity of xylem vessels, physiological and molecular consequences due to loss of COMT on root growth and adaptation to water deficit remain unexplored. We addressed this gap by evaluating the root morphology, anatomy and transcriptome of bmr12 mutant. The mutant had reduced lateral root density (LRD) and altered root anatomy and response to water limitation. The wild-type exhibits similar phenotypes under water stress, suggesting that bmr12 may be in a water deficit responsive state even in well-watered conditions. bmr12 had increased transcript abundance of genes involved in (a)biotic stress response, gibberellic acid (GA) biosynthesis and signaling. We show that bmr12 is more sensitive to exogenous GA application and present evidence for the role of GA in regulating reduced LRD in bmr12. These findings elucidate the phenotypic and molecular consequences of COMT deficiency under optimal and water stress environments in grasses.

Seed Priming with Phytohormones: An Effective Approach for the Mitigation of Abiotic Stress

Plants are often exposed to abiotic stresses such as drought, salinity, heat, cold, and heavy metals that induce complex responses, which result in reduced growth as well as crop yield. Phytohormones are well known for their regulatory role in plant growth and development, and they serve as important chemical messengers, allowing plants to function during exposure to various stresses. Seed priming is a physiological technique involving seed hydration and drying to improve metabolic processes prior to germination, thereby increasing the percentage and rate of germination and improving seedling growth and crop yield under normal and various biotic and abiotic stresses. Seed priming allows plants to obtain an enhanced capacity for rapidly and effectively combating different stresses. Thus, seed priming with phytohormones has emerged as an important tool for mitigating the effects of abiotic stress. Therefore, this review discusses the potential role of priming with phytohormones to mitigate the harmful effects of abiotic stresses, possible mechanisms for how mitigation is accomplished, and roles of priming on the enhancement of crop production.

Genome-wide identification of the HDAC family proteins and functional characterization of CsHD2C, a HD2-type histone deacetylase gene in tea plant (Camellia sinensis L. O. Kuntze)

The histone deacetylases (HDACs) are involved in growth, development and stress responses in many plants. However, the functions of HDACs in tea plant (Camellia sinensis L. O. Kuntze) and other woody plants remain unclear. Here, 18 CsHDAC genes were identified by genome-wide analysis in tea plant. The phylogenetic analysis demonstrated that the CsHDAC proteins were divided into three subfamilies, namely, the RPD3/HDA1 subfamily (8 members), the SIR2 subfamily (4 members) and the plant specific HD2 subfamily (6 members). The expression patterns showed that most members of CsHDACs family were regulated by different abiotic stress. High correlation was found between the expression of the CsHDACs and the accumulation of theanine, catechin, EGCG and other metabolites in tea plant. Most of the CsHDAC proteins were negative regulators. We further studied a specific gene CsHD2C (NCBI-ID: KY364373) in tea plant, which is the homolog of AtHD2C, encoded a protein of 306 aa. CsHD2C was highly expressed in leaves, young buds and stems. The transcription of CsHD2C was inhibited by ABA, NaCl and low temperature. It was found localized in the nucleus when fused with a YFP reporter gene. Overexpression of CsHD2C can rescue the phenotype related to different abiotic stresses in the mutant of AtHD2C in Arabidopsis. The stress-responsive genes RD29A, RD29B, ABI1 and ABI2 were also investigated to understand the regulating role of CsHD2C under abiotic stresses. We also found that CsHD2C could renew the change of acetylation level for histone H4 and the RNAP-II occupancy accumulation in the promoter of abiotic stress responses gene in the hd2c Arabidopsis mutant. Together, our results suggested that CsHD2C may act as a positive regulator in abiotic stress responses in tea plant.

Physiological and proteomic responses of reactive oxygen species metabolism and antioxidant machinery in mulberry (Morus alba L.) seedling leaves to NaCl and NaHCO3 stress

In this paper, the effects of 100 mM NaCl and NaHCO₃ stress on reactive oxygen species (ROS) and physiological and proteomic aspects of ROS metabolism in mulberry seedling leaves were studied. The results showed that NaCl stress had little effect on photosynthesis and respiration of mulberry seedling leaves. Superoxide dismutase (SOD) activity and the expression of related proteins in leaves increased by varying degrees, and accumulation of superoxide anion (O₂·^-) not observed. Under NaHCO₃ stress, photosynthesis and respiration were significantly inhibited, while the rate of O₂·^- production rate and H₂O₂ content increased. The activity of catalase (CAT) and the expression of CAT (W9RJ43) increased under NaCl stress. In response to NaHCO₃ stress, the activity and expression of CAT were significantly decreased, but the ability of H₂O₂ scavenging of peroxidase (POD) was enhanced. The ascorbic acid-glutathione (AsA-GSH) cycle in mulberry seedling leaves was enhancement in both NaCl and NaHCO₃ stress. The expression of 2-Cys peroxiredoxin BAS1 (2-Cys Prx BAS1), together with thioredoxin F (TrxF), thioredoxin O1 (TrxO1), thioredoxin-like protein CITRX (Trx CITRX), and thioredoxin-like protein CDSP32 (Trx CDSP32) were significantly increased under NaCl stress. Under NaHCO₃ stress, the expression of the electron donor of ferredoxin-thioredoxin reductase (FTR), together with Trx-related proteins, such as thioredoxin M (TrxM), thioredoxin M4 (TrxM4), thioredoxin X (TrxX), TrxF, and Trx CSDP32 were significantly decreased, suggesting that the thioredoxin-peroxiredoxin (Trx-Prx) pathway's function of scavenging H₂O₂ of in mulberry seedling leaves was inhibited. Taken together, under NaCl stress, excessive production of O₂·^- mulberry seedlings leaves was inhibited, and H₂O₂ was effectively scavenged by CAT, AsA-GSH cycle and Trx-Prx pathway. Under NaHCO₃ stress, despite the enhanced functions of POD and AsA-GSH cycle, the scavenging of O₂·^- by SOD was not effective, and that of H₂O₂ by CAT and Trx-Prx pathway were inhibited; and in turn, the oxidative damage to mulberry seedling leaves could not be reduced.

Overexpression of CrCOMT from Carex rigescens increases salt stress and modulates melatonin synthesis in Arabidopsis thaliana

CrCOMT, a COMT gene in Carex rigescens, was verified to enhance salt stress tolerance in transgenic Arabidopsis. High salinity severely restricts plant growth and development while melatonin can alleviate salt damage. Caffeic acid O-methyltransferase (COMT) plays an important role in regulating plant growth, development, and stress responses. COMT could also participate in melatonin biosynthesis. The objective of this study was to identify CrCOMT from Carex rigescens (Franch.) V. Krecz, a stress-tolerant grass species with a widespread distribution in north China, and to determine its physiological functions and regulatory mechanisms that impart tolerance to salt stress. The results showed that the transcription of CrCOMT exhibited different expression patterns under salt, drought, and ABA treatments. Transgenic Arabidopsis with the overexpression of CrCOMT exhibited improved growth and physiological performance under salt stress, such as higher lateral root numbers, proline level, and chlorophyll content, than in the wild type (WT). Overexpression of CrCOMT also increased dehydration tolerance in Arabidopsis. The transcription of salt response genes was more highly activated in transgenic plants than in the WT under salt stress conditions. In addition, the melatonin content in transgenic plants was higher than that in the WT after stress treatment. Taken together, our results indicated that CrCOMT may positively regulate stress responses and melatonin synthesis under salt stress.

Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach

BACKGROUND

Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress.

RESULTS

Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions.

CONCLUSION

Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.

Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers

The growing population requires sustainable, environmentally-friendly crops. The plant growth-enhancing properties of algal extracts have suggested their use as biofertilisers. The mechanism(s) by which algal extracts affect plant growth are unknown. We examined the effects of extracts from the common green seaweed Ulva intestinalis on germination and root development in the model land plant Arabidopsis thaliana. Ulva extract concentrations above 0.1% inhibited Arabidopsis germination and root growth. Ulva extract <0.1% stimulated root growth. All concentrations of Ulva extract inhibited lateral root formation. An abscisic-acid-insensitive mutant, abi1, showed altered sensitivity to germination- and root growth-inhibition. Ethylene- and cytokinin-insensitive mutants were partly insensitive to germination-inhibition. This suggests that different mechanisms mediate each effect of Ulva extract on early Arabidopsis development and that multiple hormones contribute to germination-inhibition. Elemental analysis showed that Ulva contains high levels of Aluminium ions (Al³⁺). Ethylene and cytokinin have been suggested to function in Al³⁺-mediated root growth inhibition: our data suggest that if Ulva Al³⁺ levels inhibit root growth, this is via a novel mechanism. We suggest algal extracts should be used cautiously as fertilisers, as the inhibitory effects on early development may outweigh any benefits if the concentration of extract is too high.

Transcription factor WRKY22 promotes aluminum tolerance via activation of OsFRDL4 expression and enhancement of citrate secretion in rice (Oryza sativa)

Whilst WRKY transcription factors are known to be involved in diverse plant responses to biotic stresses, their involvement in abiotic stress tolerance is poorly understood. OsFRDL4, encoding a citrate transporter, has been reported to be regulated by ALUMINUM (Al) RESISTANCE TRANSCRIPTION FACTOR 1 (ART1) in rice, but whether it is also regulated by other transcription factors is unknown. We define the role of OsWRKY22 in response to Al stress in rice by using mutation and transgenic complementation assays, and characterize the regulation of OsFRDL4 by OsWRKY22 via yeas one-hybrid, electrophoretic mobility shift assay and ChIP-quantitative PCR. We demonstrate that loss of OsWRKY22 function conferred by the oswrky22 T-DNA insertion allele causes enhanced sensitivity to Al stress, and a reduction in Al-induced citrate secretion. We next show that OsWRKY22 is localized in the nucleus, functions as a transcriptional activator and is able to bind to the promoter of OsFRDL4 via W-box elements. Finally, we find that both OsFRDL4 expression and Al-induced citrate secretion are significantly lower in art1 oswrky22 double mutants than in the respective single mutants. We conclude that OsWRKY22 promotes Al-induced increases in OsFRDL4 expression, thus enhancing Al-induced citrate secretion and Al tolerance in rice.

Physiological and Proteomic Responses of Contrasting Alfalfa (Medicago sativa L.) Varieties to PEG-Induced Osmotic Stress

Drought severely limits global plant distribution and agricultural production. Elucidating the physiological and molecular mechanisms governing alfalfa stress responses will contribute to the improvement of drought tolerance in leguminous crops. In this study, the physiological and proteomic responses of two alfalfa (Medicago sativa L.) varieties contrasting in drought tolerance, Longzhong (drought-tolerant) and Gannong No. 3 (drought-sensitive), were comparatively assayed when seedlings were exposed to -1.2 MPa polyethylene glycol (PEG-6000) treatments for 15 days. The results showed that the levels of proline, malondialdehyde (MDA), hydrogen peroxide (H2O2), hydroxyl free radical (OH•) and superoxide anion free radical (O2•-) in both varieties were significantly increased, while the root activity, the superoxide dismutase (SOD) and glutathione reductase (GR) activities, and the ratios of reduced/oxidized ascorbate (AsA/DHA) and reduced/oxidized glutathione (GSH/GSSG) were significantly decreased. The soluble protein and soluble sugar contents, the total antioxidant capability (T-AOC) and the activities of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) first increased and then decreased with the increase in treatment days. Under osmotic stress, Longzhong exhibited lower levels of MDA, H2O2, OH• and O2•- but higher levels of SOD, CAT, APX, T-AOC and ratios of AsA/DHA and GSH/GSSG compared with Gannong No.3. Using isobaric tags for relative and absolute quantification (iTRAQ), 142 differentially accumulated proteins (DAPs) were identified from two alfalfa varieties, including 52 proteins (34 up-regulated and 18 down-regulated) in Longzhong, 71 proteins (28 up-regulated and 43 down-regulated) in Gannong No. 3, and 19 proteins (13 up-regulated and 6 down-regulated) shared by both varieties. Most of these DAPs were involved in stress and defense, protein metabolism, transmembrane transport, signal transduction, as well as cell wall and cytoskeleton metabolism. In conclusion, the stronger drought-tolerance of Longzhong was attributed to its higher osmotic adjustment capacity, greater ability to orchestrate its enzymatic and non-enzymatic antioxidant systems and thus avoid great oxidative damage in comparison to Gannong No. 3. Moreover, the involvement of other pathways, including carbohydrate metabolism, ROS detoxification, secondary metabolism, protein processing, ion and water transport, signal transduction, and cell wall adjustment, are important mechanisms for conferring drought tolerance in alfalfa.

Therapeutic effect of 28-homobrassinolide on leukotriene synthesis in leukemia cells

The present study was aimed to investigate the effect of 28-homobrassinolide on leukotriene synthesis in the 2H3 cells. Cell viability was determined by using sulforhodamine B (SRB) assay. Leukotriene C4 (LTC4) and Leukotriene B4 (LTB4) were determined in the cell and cell lysates. Intracellular Ca2+ was determined in the intact cells. Phospholipases A2 (PLA2) expression was determined in the cells using immunofluorescence. LTC4 and LTB4 were tremendously increased in IgE-loaded 2H3 cells. However, these levels were significantly reduced following treatment with 28-homobrassinolide. The intracellular Ca2+ level was not altered by treatment. Expression of PLA2 was significantly reduced following treatment with 28-homobrassinolide. Taking all these data together, it is suggested that the 28-homobrassinolide may be a potential therapeutic agent to inhibit leukotriene synthesis in 2H3 cells.

Proteome characterization of copper stress responses in the roots of sorghum

Copper (Cu) is a important micronutrient for plants, but it is extremely toxic to plants at high concentration and can inactivate and disturb protein structures. To explore the Cu stress-induced tolerance mechanism, the present study was conducted on the roots of sorghum seedlings exposed to 50 and 100 µM CuSO₄ for 5 days. Accumulation of Cu increased in roots when the seedlings were treated with the highest concentration of Cu²⁺ ions (100 μM). Elevated Cu concentration provoked notable reduction of Fe, Zn, Ca, and Mn uptake in the roots of sorghum seedlings. In the proteome analysis, high-throughput two-dimensional polyacrylamide gel electrophoresis combined with MALDI-TOF-TOF MS was performed to explore the molecular responses of Cu-induced sorghum seedling roots. In two-dimensional silver-stained gels, 422 protein spots were identified in the 2-D gel whereas twenty-one protein spots (≥1.5-fold) were used to analyze mass spectrometry from Cu-induced sorghum roots. Among the 21 differentially expressed proteins, 10 proteins were increased, while 11 proteins were decreased due to the intake of Cu ions by roots of sorghum. Abundance of most of the identified proteins from the roots that function in stress response and metabolism was remarkably enhanced, while proteins involved in transcription and regulation were severely reduced. Taken together, these results imply insights into a potential molecular mechanism towards Cu stress in C₄ plant, sorghum.

Exogenous nitric oxide improves salt tolerance during establishment of Jatropha curcas seedlings by ameliorating oxidative damage and toxic ion accumulation

Jatropha curcas is an oilseed species that is considered an excellent alternative energy source for fossil-based fuels for growing in arid and semiarid regions, where salinity is becoming a stringent problem to crop production. Our working hypothesis was that nitric oxide (NO) priming enhances salt tolerance of J. curcas during early seedling development. Under NaCl stress, seedlings arising from NO-treated seeds showed lower accumulation of Na⁺ and Cl^- than those salinized seedlings only, which was consistent with a better growth for all analyzed time points. Also, although salinity promoted a significant increase in hydrogen peroxide (H₂O₂) content and membrane damage, the harmful effects were less aggressive in NO-primed seedlings. The lower oxidative damage in NO-primed stressed seedlings was attributed to operation of a powerful antioxidant system, including greater glutathione (GSH) and ascorbate (AsA) contents as well as catalase (CAT) and glutathione reductase (GR) enzyme activities in both endosperm and embryo axis. Priming with NO also was found to rapidly up-regulate the JcCAT1, JcCAT2, JcGR1 and JcGR2 gene expression in embryo axis, suggesting that NO-induced salt responses include functional and transcriptional regulations. Thus, NO almost completely abolished the deleterious salinity effects on reserve mobilization and seedling growth. In conclusion, NO priming improves salt tolerance of J. curcas during seedling establishment by inducing an effective antioxidant system and limiting toxic ion and reactive oxygen species (ROS) accumulation.

Recent advances in proteomics of cereals

Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.

Proteomic analysis of common bean stem under drought stress using in-gel stable isotope labeling

Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants. Plants exposed to drought for 17days and control plants at the same developmental stage were included in quantitative proteomic analysis using in-gel stable isotope labeling of proteins in combination with mass spectrometry. The quantified proteins were grouped into several functional groups, mainly into energy metabolism, photosynthesis, proteolysis, protein synthesis and proteins related to defense and stress. 70kDa heat shock protein showed the greatest increase in abundance under drought of all the proteins, suggesting its role in protecting plants against stress by re-establishing normal protein conformations and thus cellular homeostasis. The abundance of proteins involved in protein synthesis also increased under drought stress, important for recovery of damaged proteins involved in the plant cell's metabolic activities. Other important proteins in this study were related to proteolysis and folding, which are necessary for maintaining proper cellular protein homeostasis. Taken together, these results reveal the complexity of pathways involved in the drought stress response in common bean stems and enable comparison with the results of proteomic analysis of leaves, thus providing important information to further understand the biochemical and molecular mechanisms of drought response in this important legume.

Salinity-Induced Palmella Formation Mechanism in Halotolerant Algae Dunaliella salina Revealed by Quantitative Proteomics and Phosphoproteomics

Palmella stage is critical for some unicellular algae to survive in extreme environments. The halotolerant algae Dunaliella salina is a good single-cell model for studying plant adaptation to high salinity. To investigate the molecular adaptation mechanism in salinity shock-induced palmella formation, we performed a comprehensive physiological, proteomics and phosphoproteomics study upon palmella formation of D. salina using dimethyl labeling and Ti⁴⁺-immobilized metal ion affinity chromatography (IMAC) proteomic approaches. We found that 151 salinity-responsive proteins and 35 salinity-responsive phosphoproteins were involved in multiple signaling and metabolic pathways upon palmella formation. Taken together with photosynthetic parameters and enzyme activity analyses, the patterns of protein accumulation and phosphorylation level exhibited the mechanisms upon palmella formation, including dynamics of cytoskeleton and cell membrane curvature, accumulation and transport of exopolysaccharides, photosynthesis and energy supplying (i.e., photosystem II stability and activity, cyclic electron transport, and C4 pathway), nuclear/chloroplastic gene expression regulation and protein processing, reactive oxygen species homeostasis, and salt signaling transduction. The salinity-responsive protein-protein interaction (PPI) networks implied that signaling and protein synthesis and fate are crucial for modulation of these processes. Importantly, the 3D structure of phosphoprotein clearly indicated that the phosphorylation sites of eight proteins were localized in the region of function domain.

Proteomic Analysis of Tung Tree (Vernicia fordii) Oilseeds during the Developmental Stages

The tung tree (Vernicia fordii), a non-model woody plant belonging to the Euphorbiaceae family, is a promising economic plant due to the high content of a novel high-value oil in its seeds. Many metabolic pathways are active during seed development. Oil (triacylglycerols (TAGs)) accumulates in oil bodies distributed in the endosperm cells of tung tree seeds. The relationship between oil bodies and oil content during tung tree seed development was analyzed using ultrastructural observations, which confirmed that oil accumulation was correlated with the volumes and numbers of oil bodies in the endosperm cells during three different developmental stages. For a deeper understanding of seed development, we carried out proteomic analyses. At least 144 proteins were differentially expressed during three different developmental stages. A total of 76 proteins were successfully identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry/mass spectrometry (MALDI-TOF/MS/MS). These proteins were grouped into 11 classes according to their functions. The major groups of differentially expressed proteins were associated with energy metabolism (25%), fatty acid metabolism (15.79%) and defense (14.47%). These results strongly suggested that a very high percentage of gene expression in seed development is dedicated to the synthesis and accumulation of TAGs.

Ectopic over-expression of BoHO1, a cabbage heme oxygenase gene, improved salt tolerance in Arabidopsis: A case study on proteomic analysis

Plant heme oxygenase (HO) catalyzes the oxygenation of heme to biliverdin, carbon monoxide, and free iron, and is regarded as a stress-responsive protein. Here, a cabbage HO1 gene (named as BoHO1) was isolated and characterized. BoHO1 shares a high degree homology with Arabidopsis AtHO1, and could locate in Arabidopsis chloroplast. BoHO1 mRNA was ubiquitously expressed in cabbage tissues, and was responsive to several stimuli and chemicals. Genetic evidence illustrated that over-expression of BoHO1 in transgenic Arabidopsis plants (35S:BoHO1-1 and 35S:BoHO1-2) significantly alleviated salinity stress-inhibited seedling growth, which were accompanied with the re-establishment of reactive oxygen species and ion homeostasis. Comparative proteomic analysis was subsequently performed. Results revealed that protein abundance related to light reactions was greatly suppressed by NaCl stress in wild-type, whereas was partially recovered in 35S:BoHO1-1. Salinity stress also strongly activated stress-related metabolic processes in wild-type, i.e. carbon and energy metabolism, ammonium detoxification, and protein turnover, and these induced tendencies were more intensive in 35S:BoHO1-1. Particularly, proteins related to glutathione metabolism and ion homeostasis were specifically enriched in NaCl-stressed 35S:BoHO1-1. On the basis of above results, we propose that BoHO1 could activate multiple stress-responsive pathways to help Arabidopsis regain cellular homeostasis, thus presenting enhanced adaptation to salinity stress.

Role of the proteome in phytohormonal signaling

Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Proteome profile of salt gland-rich epidermis extracted from a salt-tolerant tree species

Preparation of proteins from salt-gland-rich tissues of mangrove plant is necessary for a systematic study of proteins involved in the plant's unique desalination mechanism. Extraction of high-quality proteins from the leaves of mangrove tree species, however, is difficult due to the presence of high levels of endogenous phenolic compounds. In our study, preparation of proteins from only a part of the leaf tissues (i.e. salt gland-rich epidermal layers) was required, rendering extraction even more challenging. By comparing several extraction methods, we developed a reliable procedure for obtaining proteins from salt gland-rich tissues of the mangrove species Avicennia officinalis. Protein extraction was markedly improved using a phenol-based extraction method. Greater resolution 1D protein gel profiles could be obtained. More promising proteome profiles could be obtained through 1D-LC-MS/MS. The number of proteins detected was twice as much as compared to TUTS extraction method. Focusing on proteins that were solely present in each extraction method, phenol-based extracts contained nearly ten times more proteins than those in the extracts without using phenol. The approach could thus be applied for downstream high-throughput proteomic analyses involving LC-MS/MS or equivalent. The proteomics data presented herein are available via ProteomeXchange with identifier PXD001691.

Proteomics, metabolomics, and ionomics perspectives of salinity tolerance in halophytes

Halophytes are plants which naturally survive in saline environment. They account for ∼1% of the total flora of the world. They include both dicots and monocots and are distributed mainly in arid, semi-arid inlands and saline wet lands along the tropical and sub-tropical coasts. Salinity tolerance in halophytes depends on a set of ecological and physiological characteristics that allow them to grow and flourish in high saline conditions. The ability of halophytes to tolerate high salt is determined by the effective coordination between various physiological processes, metabolic pathways and protein or gene networks responsible for delivering salinity tolerance. The salinity responsive proteins belong to diverse functional classes such as photosynthesis, redox homeostasis; stress/defense, carbohydrate and energy metabolism, protein metabolism, signal transduction and membrane transport. The important metabolites which are involved in salt tolerance of halophytes are proline and proline analog (4-hydroxy-N-methyl proline), glycine betaine, pinitol, myo-inositol, mannitol, sorbitol, O-methylmucoinositol, and polyamines. In halophytes, the synthesis of specific proteins and osmotically active metabolites control ion and water flux and support scavenging of oxygen radicals under salt stress condition. The present review summarizes the salt tolerance mechanisms of halophytes by elucidating the recent studies that have focused on proteomic, metabolomic, and ionomic aspects of various halophytes in response to salinity. By integrating the information from halophytes and its comparison with glycophytes could give an overview of salt tolerance mechanisms in halophytes, thus laying down the pavement for development of salt tolerant crop plants through genetic modification and effective breeding strategies.

Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress

Salinity is a limiting factor affecting crop growth. We evaluated the responses of a salt-tolerant recombinant inbred rice (Oryza sativa L.) line, FL478, and the salt-sensitive IR29. Seedlings were exposed to salt stress and the growth rate was monitored to decipher the effect of long-term stress. At Day 16, IR29 produced lower shoot biomass than FL478. Significant differences for Na+ and K+ concentrations and Na+ : K+ ratios in roots and shoots were observed between genotypes. Changes in the proteomes of control and salt-stressed plants were analysed, identifying 59 and 39 salt-responsive proteins in roots and leaves, respectively. Proteomic analysis showed greater downregulation of proteins in IR29. In IR29, proteins related to pathways involved in salt tolerance (e.g. oxidative stress response, amino acid biosynthesis, polyamine biosynthesis, the actin cytoskeleton and ion compartmentalisation) changed to combat salinity. We found significant downregulation of proteins related to photosynthetic electron transport in IR29, indicating that photosynthesis was influenced, probably increasing the risk of reactive oxygen species formation. The sensitivity of IR29 might be related to its inability to exclude salt from its transpiration stream, to compartmentalise excess ions and to maintain a healthy photosynthetic apparatus during salt stress, or might be because of the leakiness of its roots, allowing excess salt to enter apoplastically. In FL478, superoxide dismutase, ferredoxin thioredoxin reductase, fibre protein and inorganic pyrophosphatase, which may participate in salt tolerance, increased in abundance. Our analyses provide novel insights into the mechanisms behind salt tolerance and sensitivity in genotypes with close genetic backgrounds.

Cell Wall Metabolism in Response to Abiotic Stress

This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions.

Plant exomics: concepts, applications and methodologies in crop improvement

Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.

Identification of early salt stress responsive proteins in seedling roots of upland cotton (Gossypium hirsutum L.) employing iTRAQ-based proteomic technique

Soil salinity is a major abiotic stress that limits plant growth and agricultural productivity. Upland cotton (Gossypium hirsutum L.) is highly tolerant to salinity; however, large-scale proteomic data of cotton in response to salt stress are still scant. Here, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic technique was employed to identify the early differentially expressed proteins (DEPs) from salt-treated cotton roots. One hundred and twenty-eight DEPs were identified, 76 of which displayed increased abundance and 52 decreased under salt stress conditions. The majority of the proteins have functions related to carbohydrate and energy metabolism, transcription, protein metabolism, cell wall and cytoskeleton metabolism, membrane and transport, signal transduction, in addition to stress and defense. It is worth emphasizing that some novel salt-responsive proteins were identified, which are involved in cell cytoskeleton metabolism (actin-related protein2, ARP2, and fasciclin-like arabinogalactan proteins, FLAs), membrane transport (tonoplast intrinsic proteins, TIPs, and plasma membrane intrinsic proteins, PIPs), signal transduction (leucine-rich repeat receptor-like kinase encoding genes, LRR-RLKs) and stress responses (thaumatin-like protein, TLP, universal stress protein, USP, dirigent-like protein, DIR, desiccation-related protein PCC13-62). High positive correlation between the abundance of some altered proteins (superoxide dismutase, SOD, peroxidase, POD, glutathione S-transferase, GST, monodehydroascorbate reductase, MDAR, and malate dehydrogenase, MDH) and their enzyme activity was evaluated. The results demonstrate that the iTRAQ-based proteomic technique is reliable for identifying and quantifying a large number of cotton root proteins. qRT-PCR was used to study the gene expression levels of the five above-mentioned proteins; four patterns are consistent with those of induced protein. These results showed that the proteome of cotton roots under NaCl stress is complex. The comparative protein profiles of roots under salinity vs control improves the understanding of the molecular mechanisms involved in the tolerance of plants to salt stress. This work provides a good basis for further functional elucidation of these DEPs using genetic and/or other approaches, and, consequently, candidate genes for genetic engineering to improve crop salt tolerance.

Proteomics of seed development, desiccation tolerance, germination and vigor

Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.

Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR

Next generation sequencing (NGS) technologies have been used to generate huge amounts of sequencing data from many organisms. However, the correct choice of candidate genes and prevention of false-positive results computed from digital gene expression (DGE) of RNA-seq data are vital when using these genetic resources. We indirectly identified 18 salt-stress-induced Reaumuria trigyna transcripts from the transcriptome sequencing data using differential-display reverse transcription PCR (DDRT-PCR) combined with local BLAST searches. Highly consistent with the DGE results, the quantitative real-time PCR expression patterns of these transcripts showed strong upregulation by salt stress, suggesting that these genes may play important roles in R. trigyna's survival under high-salt environments. The method presented here successfully identified responsive genes from the massive amount of RNA-seq data. Thus, we suggest that DDRT-PCR could be employed to mine NGS data in a wide range of applications in transcriptomic studies. In addition, the genes identified in the present study are promising candidates for further elucidation of the salt tolerance mechanisms in R. trigyna.

Involvement of abscisic acid in the response of Medicago sativa plants in symbiosis with Sinorhizobium meliloti to salinity

Legumes are classified as salt-sensitive crops with their productivity particularly affected by salinity. Abcisic acid (ABA) plays an important role in the response to environmental stresses as signal molecule which led us to study its role in the response of nitrogen fixation and antioxidant metabolism in root nodules of Medicago sativa under salt stress conditions. Adult plants inoculated with Sinorhizobium meliloti were treated with 1 μM and 10 μM ABA two days before 200 mM salt addition. Exogenous ABA together with the salt treatment provoked a strong induction of the ABA content in the nodular tissue which alleviated the inhibition induced by salinity in the plant growth and nitrogen fixation. Antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) were induced by ABA pre-treatments under salt stress conditions which together with the reduction of the lipid peroxidation, suggest a role for ABA as signal molecule in the activation of the nodular antioxidant metabolism. Interaction between ABA and polyamines (PAs), described as anti-stress molecules, was studied being detected an induction of the common polyamines spermidine (Spd) and spermine (Spm) levels by ABA under salt stress conditions. In conclusion, ABA pre-treatment improved the nitrogen fixation capacity under salt stress conditions by the induction of the nodular antioxidant defenses which may be mediated by the common PAs Spd and Spm that seems to be involved in the anti-stress response induced by ABA.