Rice ASR1 and ASR5 are complementary transcription factors regulating aluminium responsive genes

Comparative transcriptome analyses reveal regulatory network and hub genes of aluminum response in roots of elephant grass (Cenchrus purpureus)

Aluminum (Al) toxicity severely restricts the growth and productivity of elephant grass in acidic soils around the world. However, the molecular mechanisms of Al response have not been investigated in elephant grass. In this study, we conducted phenotype, physiology, and transcriptome analysis of elephant grass roots in response to Al stress. Phenotypic analysis revealed that a low concentration of Al stress improved root growth while higher Al concentrations inhibit root growth. Al stress significantly increased the citrate (CA) content in roots, while the expression levels of genes related to citrate synthesis were substantially changed. The multidrug and toxic compound extrusion (MATE) family were identified as hub genes in the co-expression network of Al response in elephant grass roots. Phylogenetic analysis showed that hub genes CpMATE93 and CpMATE158 belonged to the same clade as other MATE genes reported to be involved in citrate transport. Additionally, overexpression of CpMATE93 conferred Al resistance in yeast cells. These results provide a theoretical basis for further studies of molecular mechanisms in the elephant grass response to Al stress and could help breeders develop elite cultivars with Al tolerance.

Gibberellin-Mediated Sensitivity of Rice Roots to Aluminum Stress

Aluminum toxicity poses a significant constraint on crop production in acidic soils. While phytohormones are recognized for their pivotal role in mediating plant responses to aluminum stress, the specific involvement of gibberellin (GA) in regulating aluminum tolerance remains unexplored. In this study, we demonstrate that external GA exacerbates the inhibitory impact of aluminum stress on root growth of rice seedlings, concurrently promoting reactive oxygen species (ROS) accumulation. Furthermore, rice plants overexpressing the GA synthesis gene SD1 exhibit enhanced sensitivity to aluminum stress. In contrast, the slr1 gain-of-function mutant, characterized by impeded GA signaling, displays enhanced tolerance to aluminum stress, suggesting the negative regulatory role of GA in rice resistance to aluminum-induced toxicity. We also reveal that GA application suppresses the expression of crucial aluminum tolerance genes in rice, including Al resistance transcription factor 1 (ART1), Nramp aluminum transporter 1 (OsNramp4), and Sensitive to Aluminum 1 (SAL1). Conversely, the slr1 mutant exhibits up-regulated expression of these genes compared to the wild type. In summary, our results shed light on the inhibitory effect of GA in rice resistance to aluminum stress, contributing to a theoretical foundation for unraveling the intricate mechanisms of plant hormones in regulating aluminum tolerance.

Identification of the Abscisic Acid-, Stress-, and Ripening-Induced (ASR) Family Involved in the Adaptation of Tetragonia tetragonoides (Pall.) Kuntze to Saline-Alkaline and Drought Habitats

Tetragonia tetragonoides (Pall.) Kuntze (Aizoaceae, 2n = 2x = 32), a vegetable used for both food and medicine, is a halophyte that is widely distributed in the coastal areas of the tropics and subtropics. Saline-alkaline soils and drought stress are two major abiotic stressors that significantly affect the distribution of tropical coastal plants. Abscisic acid-, stress-, and ripening-induced (ASR) proteins belong to a family of plant-specific, small, and hydrophilic proteins with important roles in plant development, growth, and abiotic stress responses. Here, we characterized the ASR gene family from T. tetragonoides, which contained 13 paralogous genes, and divided TtASRs into two subfamilies based on the phylogenetic tree. The TtASR genes were located on two chromosomes, and segmental duplication events were illustrated as the main duplication method. Additionally, the expression levels of TtASRs were induced by multiple abiotic stressors, indicating that this gene family could participate widely in the response to stress. Furthermore, several TtASR genes were cloned and functionally identified using a yeast expression system. Our results indicate that TtASRs play important roles in T. tetragonoides' responses to saline-alkaline soils and drought stress. These findings not only increase our understanding of the role ASRs play in mediating halophyte adaptation to extreme environments but also improve our knowledge of plant ASR protein evolution.

Genetic-based dissection of resistance to bacterial leaf streak in rice by GWAS

BACKGROUND

Rice is the second-largest food crop in the world and vulnerable to bacterial leaf streak disease. A thorough comprehension of the genetic foundation of agronomic traits was essential for effective implementation of molecular marker-assisted selection.

RESULTS

Our study aimed to evaluate the vulnerability of rice to bacterial leaf streak disease (BLS) induced by the gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc). In order to accomplish this, we first analyzed the population structure of 747 accessions and subsequently assessed their phenotypes 20 days after inoculation with a strain of Xoc, GX01. We conducted genome-wide association studies (GWAS) on a population of 747 rice accessions, consisting of both indica and japonica subpopulations, utilizing phenotypic data on resistance to bacterial leaf streak (RBLS) and sequence data. We identified a total of 20 QTLs associated with RBLS in our analysis. Through the integration of linkage mapping, sequence analysis, haplotype analysis, and transcriptome analysis, we were able to identify five potential candidate genes (OsRBLS1-OsRBLS5) that possess the potential to regulate RBLS in rice. In order to gain a more comprehensive understanding of the genetic mechanism behind resistance to bacterial leaf streak, we conducted tests on these genes in both the indica and japonica subpopulations, ultimately identifying superior haplotypes that suggest the potential utilization of these genes in breeding disease-resistant rice varieties.

CONCLUSIONS

The findings of our study broaden our comprehension of the genetic mechanisms underlying RBLS in rice and offer significant insights that can be applied towards genetic improvement and breeding of disease-resistant rice in rapidly evolving environmental conditions.

Two Sweet Sorghum (Sorghum bicolor L.) WRKY Transcription Factors Promote Aluminum Tolerance via the Reduction in Callose Deposition

Aluminum (Al) toxicity is a primary limiting factor for crop production in acidic soils. The WRKY transcription factors play important roles in regulating plant growth and stress resistance. In this study, we identified and characterized two WRKY transcription factors, SbWRKY22 and SbWRKY65, in sweet sorghum (Sorghum bicolor L.). Al induced the transcription of SbWRKY22 and SbWRKY65 in the root apices of sweet sorghum. These two WRKY proteins were localized in the nucleus and exhibited transcriptional activity. SbWRKY22 showed the significant transcriptional regulation of SbMATE, SbGlu1, SbSTAR1, SbSTAR2a, and SbSTAR2b, which are major known Al tolerance genes in sorghum. Interestingly, SbWRKY65 had almost no effect on the aforementioned genes, but it significantly regulated the transcription of SbWRKY22. Therefore, it is speculated that SbWRKY65 might indirectly regulate Al-tolerance genes mediated by SbWRKY22. The heterologous expression of SbWRKY22 and SbWRKY65 greatly improved the Al tolerance of transgenic plants. The enhanced Al tolerance phenotype of transgenic plants is associated with reduced callose deposition in their roots. These findings suggest the existence of SbWRKY22- and SbWRKY65-mediated Al tolerance regulation pathways in sweet sorghum. This study extends our understanding of the complex regulatory mechanisms of WRKY transcription factors in response to Al toxicity.

Aluminum in plant: Benefits, toxicity and tolerance mechanisms

Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.

LEAfing through literature: late embryogenesis abundant proteins coming of age-achievements and perspectives

To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review, we summarize current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, post-translational modifications, or water deprivation, we provide a detailed summary of current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil to helix transitions, self-assembly, and their recently discovered ability to undergo liquid-liquid phase separation. We point out the promising potential of LEA proteins in biotechnological and agronomic applications, and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity.

A zinc finger protein SlSZP1 protects SlSTOP1 from SlRAE1-mediated degradation to modulate aluminum resistance

In acidic soils, aluminum (Al) toxicity is the main factor inhibiting plant root development and reducing crops yield. STOP1 (SENSITIVE TO PROTON RHIZOTOXICITY 1) was a critical factor in detoxifying Al stress. Under Al stress, STOP1 expression was not induced, although STOP1 protein accumulated, even in the presence of RAE1 (STOP1 DEGRADATION E3-LIGASE). How the Al stress triggers and stabilises the accumulation of STOP1 is still unknown. Here, we characterised SlSTOP1-interacting zinc finger protein (SlSZP1) using a yeast-two-hybrid screening, and generated slstop1, slszp1 and slstop1/slszp1 knockout mutants using clustered regularly interspaced short palindromic repeats (CRISPR) in tomato. SlSZP1 is induced by Al stress but it is not regulated by SlSTOP1. The slstop1, slszp1 and slstop1/slszp1 knockout mutants exhibited hypersensitivity to Al stress. The expression of SlSTOP1-targeted genes, such as SlRAE1 and SlASR2 (ALUMINUM SENSITIVE), was inhibited in both slstop1 and slszp1 mutants, but not directly regulated by SlSZP1. Furthermore, the degradation of SlSTOP1 by SlRAE1 was prevented by SlSZP1. Al stress increased the accumulation of SlSTOP1 in wild-type (WT) but not in slszp1 mutants. The overexpression of either SlSTOP1 or SlSZP1 did not enhance plant Al resistance. Altogether, our results show that SlSZP1 is an important factor for protecting SlSTOP1 from SlRAE1-mediated degradation.

Metabolome Analysis under Aluminum Toxicity between Aluminum-Tolerant and -Sensitive Rice (Oryza sativa L.)

Aluminum (Al) solubilizes into trivalent ions (Al³⁺) on acidic soils, inhibiting root growth. Since about 13% of global rice cultivation is grown on acidic soils, improving Al tolerance in rice may significantly increase yields. In the present study, metabolome analysis under Al toxicity between the Al-tolerant variety Nipponbare and the Al-sensitive variety H570 were performed. There were 45 and 83 differential metabolites which were specifically detected in Nipponbare and H570 under Al toxicity, respectively. Furthermore, the results showed that 16 lipids out of 45 total metabolites were down-regulated, and 7 phenolic acids as well as 4 alkaloids of 45 metabolites were up-regulated in Nipponbare, while 12 amino acids and their derivatives were specifically detected in H570, of which 11 amino acids increased, including L-homoserine and L-methionine, which are involved in cysteine synthesis, L-ornithine and L-proline, which are associated with putrescine synthesis, and 1-aminocyclopropane-1-carboxylate, which is associated with ethylene synthesis. The contents of cysteine and s-(methyl) glutathione, which were reported to be related to Al detoxification in rice, decreased significantly. Meanwhile, putrescine was accumulated in H570, while there was no significant change in Nipponbare, so we speculated that it might be an intermediate product of Al detoxification in rice. The differential metabolites detected between Al-tolerant and -sensitive rice variants in the present study might play important roles in Al tolerance. These results provide new insights in the mechanisms of Al tolerance in rice.

Grape ASR Regulates Glucose Transport, Metabolism and Signaling

To decipher the mediator role of the grape Abscisic acid, Stress, Ripening (ASR) protein, VvMSA, in the pathways of glucose signaling through the regulation of its target, the promoter of hexose transporter VvHT1, we overexpressed and repressed VvMSA in embryogenic and non-embryogenic grapevine cells. The embryogenic cells with organized cell proliferation were chosen as an appropriate model for high sensitivity to the glucose signal, due to their very low intracellular glucose content and low glycolysis flux. In contrast, the non-embryogenic cells displaying anarchic cell proliferation, supported by high glycolysis flux and a partial switch to fermentation, appeared particularly sensitive to inhibitors of glucose metabolism. By using different glucose analogs to discriminate between distinct pathways of glucose signal transduction, we revealed VvMSA positioning as a transcriptional regulator of the glucose transporter gene VvHT1 in glycolysis-dependent glucose signaling. The effects of both the overexpression and repression of VvMSA on glucose transport and metabolism via glycolysis were analyzed, and the results demonstrated its role as a mediator in the interplay of glucose metabolism, transport and signaling. The overexpression of VvMSA in the Arabidopsis mutant abi8 provided evidence for its partial functional complementation by improving glucose absorption activity.

Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins

In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.

Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits

The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.

Mechanisms underlying the phytotoxicity and genotoxicity of aluminum and their alleviation strategies: A review

Aluminum (Al) is considered as a potential limiting factor for plant growth in acidic environment. At lower concentration, Al promotes plant growth by facilitating the phosphorous availability, while, at higher concentration, it causes rhizotoxicity by inhibiting the nutrient transportation system. Cellular membrane is identified as the first site of Al toxicity, which is consequent to Al-induced reactive oxygen species prompted lipid catabolism. Among all the soluble forms, the trivalent cationic form (Al³⁺) of Al is most toxic. Though, the ability to ascribe Al-tolerance is very complex, exclusion is an extensively established process contributing to Al³⁺ detoxification. Alteration in pH at root apex/rhizosphere, exudation of chelating agents, cell wall immobilization, and Al efflux have been recognized as probable methods for exclusion of Al, which is highly dependent on concentrations of organic acids, and plant species. Additionally, exogenous applications of boron, silicon, calcium, etc., in Al-stressed plant species can form a conjugate with it, thereby reducing its bioavailability/toxicity. Moreover, nanoparticles (NPs) are emerging tools in agricultural sector, which are found to be relatively more effective in mitigation of metal stress compared to their bulk materials. This review exhibits the fundamental approaches of Al phytotoxicity and endows with a comprehensive knowledge of the cellular and metabolic processes underlying toxic impacts along with ameliorative efficiencies of various potential agents including NPs. Additionally, it also elucidates the molecular mechanisms, future research prospects and challenges in effective alleviation mechanisms for enhancing plant Al-tolerance, to improve the growth and yields of susceptible-species on acidic soil.

Phytohormone signalling and cross-talk to alleviate aluminium toxicity in plants

Aluminium (Al) is one of the most abundant metals in earth crust, which becomes toxic to the plants growing in acidic soil. Phytohormones like ethylene, auxin, cytokinin, abscisic acid, jasmonic acid and gibberellic acid are known to play important role in regulating Al toxicity tolerance in plants. Exogenous applications of auxin, cytokinin and abscisic acid have shown significant effect on Al-induced root growth inhibition. Moreover, ethylene and cytokinin act synergistically with auxin in responding against Al toxicity. A number of studies showed that phytohormones play vital roles in controlling root responses to Al toxicity by modulating reactive oxygen species (ROS) signalling, cell wall modifications, organic acid exudation from roots and expression of Al responsive genes and transcription factors. This review provides a summary of recent studies related to involvement of phytohormone signalling and cross-talk with other pathways in regulating response against Al toxicity in plants.

TaASR1-D confers abiotic stress resistance by affecting ROS accumulation and ABA signalling in transgenic wheat

Cultivating new crop cultivars with multiple abiotic stress tolerances is important for crop production. The abscisic acid-stress-ripening (ASR) protein has been shown to confer abiotic stress tolerance in plants. However, the mechanisms of ASR function under stress condition remain largely unclear. In this study, we characterized all ASR family members in common wheat and constitutively overexpressed TaASR1-D in a commercial hexaploid wheat cultivar Zhengmai 9023. The transgenic wheat plants exhibited increased tolerance to multiple abiotic stresses and increased grain yields under salt stress condition. Overexpression of TaASR1-D conferred enhanced antioxidant capacity and ABA sensitivity in transgenic wheat plants. Further, RNA in situ hybridization results showed that TaASR1-D had higher expression levels in the vascular tissues of leaves and the parenchyma cells around the vascular tissues of roots and stems. Yeast one-hybrid and electrophoretic mobility shift assays revealed that TaASR1-D could directly bind the specific cis-elements in the promoters of TaNCED1 and TaGPx1-D. In conclusion, our findings suggest that TaASR1-D can be used to breed new wheat cultivars with increased multiple abiotic stress tolerances, and TaASR1-D enhances abiotic stress tolerances by reinforcing antioxidant capacity and ABA signalling.

Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum

Background

Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils.

Methods

Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress.

Results

Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.

OsGERLP: A novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia

There is a decrease in the land available for rice cultivation due to the rapid conversion to urban uses. Subsequently, acid soil could be an alternative land cultivating rice, but will require the use of aluminum (Al)-tolerant rice varieties. This Al tolerance trait is genetically controlled, and there is a need to discover more genes needed to develop Al-tolerant rice. Therefore, the objective of this study was to clone and characterize a novel Al tolerance gene isolated from a local cultivar of Indonesian rice. The gene cloning was conducted based on the rye/rice microsynteny relationship. In addition, the root growth and gene expression analyses were performed to verify the role of the gene on Al tolerance in gene-silenced rice and in overexpressed transgenic tobacco. The results showed an Al tolerance candidate gene, OsGERLP, was successfully cloned from rice cv. Hawara Bunar, with its gene encoding a protein similar to a bacterial ribosomal L32 protein. Additionally, the analysis showed that low gene expression caused the gene-silenced rice to be sensitive to Al, while high expression induced the Al tolerance in transgenic tobacco. Furthermore, it was discovered that the gene expression level in both plants was in line with the lower expression of the OsFRDL4 gene in the silenced rice and the high expression of the MATE gene in transgenic tobacco also with the higher citrate secretion from transgenic tobacco roots. In conclusion, the OsGERLP gene could act as a regulator for other Al tolerance genes, with the potential to develop Al-tolerant rice varieties.

The role of solute transporters in aluminum toxicity and tolerance

The prevalence of aluminum ions (Al³⁺ ) under acidic soil conditions inhibits primary root elongation and hinders plant growth and productivity. Al³⁺ alters the membrane potential, displaces critical ions in the apoplast and disrupts intracellular ionic concentrations by targeting membrane-localized solute transporters. Here, we provide an overview of how Al³⁺ affects the activities of several solute transporters especially in the root. High Al³⁺ level impairs the functions of potassium (K⁺ ), calcium (Ca²⁺ ), magnesium (Mg²⁺ ), nitrate (NO₃ ^- ) and ammonium (NH₄ ⁺ ) transporters. We further discuss the role of some key transporters in mediating Al tolerance either by exclusion or sequestration. Anion channels responsible for organic acid efflux modulate the sensitivity to Al³⁺ . The ALUMINUM ACTIVATED MALATE TRANSPORTER (ALMT) and MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) family of transporters exude malate and citrate, respectively, to the rhizosphere to alleviate Al toxicity by Al exclusion. The ABC transporters, aquaporins and H⁺ -ATPases perform vacuolar sequestration of Al³⁺ , leading to aluminum tolerance in plants. Targeting these solute transporters in crop plants can help generating aluminum-tolerant crops in future.

Structural and Functional Characterization of the ABA-Water Deficit Stress Domain from Wheat and Barley: An Intrinsically Disordered Domain behind the Versatile Functions of the Plant Abscissic Acid, Stress and Ripening Protein Family

The ASR protein family has been discovered thirty years ago in many plant species and is involved in the tolerance of various abiotic stresses such as dehydration, salinity and heat. Despite its importance, nothing is known about the conserved ABA-Water Deficit Stress Domain (ABA-WDS) of the ASR gene family. In this study, we characterized two ABA-WDS domains, isolated from durum wheat (TtABA-WDS) and barley (HvABA-WDS). Bioinformatics analysis shows that they are both consistently predicted to be intrinsically disordered. Hydrodynamic and circular dichroism analysis indicate that both domains are largely disordered but belong to different structural classes, with HvABA-WDS and TtABA-WDS adopting a PreMolten Globule-like (PMG-like) and a Random Coil-like (RC-like) conformation, respectively. In the presence of the secondary structure stabilizer trifluoroethanol (TFE) or of increasing glycerol concentrations, which mimics dehydration, the two domains acquire an α-helical structure. Interestingly, both domains are able to prevent heat- and dehydration-induced inactivation of the enzyme lactate dehydrogenase (LDH). Furthermore, heterologous expression of TtABA-WDS and HvABA-WDS in the yeast Saccharomyces cerevisiae improves its tolerance to salt, heat and cold stresses. Taken together our results converge to show that the ABA-WDS domain is an intrinsically disordered functional domain whose conformational plasticity could be instrumental to support the versatile functions attributed to the ASR family, including its role in abiotic stress tolerance. Finally, and after validation in the plant system, this domain could be used to improve crop tolerance to abiotic stresses.

A novel wheat ASR gene, TaASR2D, enhances drought tolerance in Brachypodium distachyon

Abscisic acid-, stress-, and ripening-induced (ASR) proteins play an important role in protecting plants against adverse environmental conditions. Here, we identified 24 ASR genes in the wheat genome and analyzed their characteristics. Among these, five ASR genes highly induced by abscisic acid (ABA) and polyethylene glycol were cloned and further characterized. The TaASR genes were expressed in response to different abiotic stresses and ABA and were found to be localized in the nucleus and plasma membrane of transformed tobacco cells. Brachypodium distachyon transgenic plants overexpressing TaASR2D showed enhanced drought tolerance by regulating leaf transpiration. The expression levels of stress-related and ABA-responsive genes were higher in transgenic plants than in wild-type plants under drought stress conditions. Moreover, overexpression of TaASR2D increased the levels of both endogenous ABA and hydrogen peroxide in response to drought stress, and these plants showed hypersensitivity to exogenous ABA at the germination stage. Furthermore, plants overexpressing TaASR2D showed increased stomatal closure. Further analysis revealed that TaASR2D interacts with ABA biosynthesis and stress-related proteins in yeast and tobacco plants. Collectively, these findings indicate that TaASR2D plays an important role in the response of plants to drought stress by regulating the ABA biosynthesis pathway and redox homeostasis system.

Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils

Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.

CaASR1 promotes salicylic acid- but represses jasmonic acid-dependent signaling to enhance the resistance of Capsicum annuum to bacterial wilt by modulating CabZIP63

CabZIP63 acts positively in the resistance of pepper (Capsicum annuum) to bacterial wilt caused by Ralstonia solanacearum or tolerance to high-temperature/high-humidity stress, but it is unclear how CabZIP63 achieves its functional specificity against R. solanacearum. Here, CaASR1, an abscisic acid-, stress-, and ripening-inducible protein of C. annuum, was functionally characterized in modulating the functional specificity of CabZIP63 during the defense response of pepper to R. solanacearum. In pepper plants inoculated with R. solanacearum, CaASR1 was up-regulated before 24 h post-inoculation but down-regulated thereafter, and was down-regulated by high-temperature/high-humidity stress. Data from gene silencing and transient overexpression experiments indicated that CaASR1 acts as a positive regulator in the immunity of pepper against R. solanacearum and a negative regulator of thermotolerance. Pull-down combined with mass spectrometry revealed that CaASR1 interacted with CabZIP63 upon R. solanacearum infection; the interaction was confirmed by microscale thermophoresis and bimolecular fluorescence complementation assays.CaASR1 silencing upon R. solanacearum inoculation repressed CabZIP63-mediated transcription from the promoters of the salicylic acid (SA)-dependent CaPR1 and CaNPR1, but derepressed transcription of CaHSP24 and the jasmonic acid (JA)-dependent CaDEF1. Our findings suggest that CaASR1 acts as a positive regulator of the defense response of pepper to R. solanacearum by interacting with CabZIP63, enabling it to promote SA-dependent but repress JA-dependent immunity and thermotolerance during the early stages of infection.

A WRKY transcription factor confers aluminum tolerance via regulation of cell wall modifying genes

Modification of cell wall properties has been considered as one of the determinants that confer aluminum (Al) tolerance in plants, while how cell wall modifying processes are regulated remains elusive. Here, we present a WRKY transcription factor WRKY47 involved in Al tolerance and root growth. Lack of WRKY47 significantly reduces, while overexpression of it increases Al tolerance. We show that lack of WRKY47 substantially affects subcellular Al distribution in the root, with Al content decreased in apoplast and increased in symplast, which is attributed to the reduced cell wall Al-binding capacity conferred by the decreased content of hemicellulose I in the wrky47-1 mutant. Based on microarray, real time-quantitative polymerase chain reaction and chromatin immunoprecipitation assays, we further show that WRKY47 directly regulates the expression of EXTENSIN-LIKE PROTEIN (ELP) and XYLOGLUCAN ENDOTRANSGLUCOSYLASE-HYDROLASES17 (XTH17) responsible for cell wall modification. Increasing the expression of ELP and XTH17 rescued Al tolerance as well as root growth in wrky47-1 mutant. In summary, our results demonstrate that WRKY47 is required for root growth under both normal and Al stress conditions via direct regulation of cell wall modification genes, and that the balance of Al distribution between root apoplast and symplast conferred by WRKY47 is important for Al tolerance.

AtHB7/12 Regulate Root Growth in Response to Aluminum Stress

Aluminum (Al) stress is a major limiting factor for plant growth and crop production in acid soils. At present, only a few transcription factors involved in the regulation of Al resistance have been characterized. Here, we used reversed genetic approach through phenotype analysis of overexpressors and mutants to demonstrate that AtHB7 and AtHB12, two HD-Zip I transcription factors, participate in Al resistance. In response to Al stress, AtHB7 and AtHB12 displayed different dynamic expression patterns. Although both AtHB7 and AtHB12 positively regulate root growth in the absence of Al stress, our results showed that AtHB7 antagonizes with AtHB12 to control root growth in response to Al stress. The athb7/12 double mutant displayed a wild-type phenotype under Al stress. Consistently, our physiological analysis showed that AtHB7 and AtHB12 oppositely regulate the capacity of cell wall to bind Al. Yeast two hybrid assays showed that AtHB7 and AtHB12 could form homo-dimers and hetero-dimers in vitro, suggesting the interaction between AtHB7 and AtHB12 in the regulation of root growth. The conclusion was that AtHB7 and AtHB12 oppositely regulate Al resistance by affecting Al accumulation in root cell wall.

Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.)

BACKGROUND

Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet.

METHODS

We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively.

RESULTS

In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress.

CONCLUSION

We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.

The effects of exogenous malic acid in relieving aluminum toxicity in Pinus massoniana

Two different genotypes of Pinus massoniana seedlings (aluminum-resistant FJ5 and aluminum-sensitive GD20) were used, the effects of different exogenous malic acid (0.00, 0.01, 0.02, 0.04, 0.08, 0.16 mmol·L^-1) on the growth attributes of P. massoniana seedlings treated by the Al³⁺ concentration of 0.8 mmol·L^-1 were studied, to provide a basis for the growth in acidified soil. In our experiment, the seedling growth was inhibited by Al³⁺ treatment. After treatment with a low concentration of exogenous malic acid, the activities of antioxidant enzymes in leaves were enhanced, the concentrations of hydrogen peroxide (H₂O₂), superoxide (O₂^-·), malondialdehyde (MDA) and osmotic adjustment substances were reduced accordingly. GD20 exhibited more severe changes compared with FJ5. The larger ones of the contribution rates of the indices in principal component analysis were H₂O₂, Glutathione Reductase (GR). These results indicated that Al³⁺ with high concentration inhibits the growth of P. massoniana. Malic acid could effectively alleviate the toxicity, and the mitigation effect on the aluminum-sensitive species, which genotype is more sensitive to the response of Al³⁺ toxicity, was more effective than that on the aluminum-resistant. How to select and cultivate more resistant species, by using the main parameter (H₂O₂ and GR), is worthy in further study.

A Maize ZmAT6 Gene Confers Aluminum Tolerance via Reactive Oxygen Species Scavenging

Aluminum (Al) toxicity is the primary limiting factor that affects crop yields in acid soil. However, the genes that contribute to the Al tolerance process in maize are still poorly understood. Previous studies have predicted that ZmAT6 is a novel protein which could be upregulated under Al stress condition. Here, we found that ZmAT6 is expressed in many tissues and organs and can be dramatically induced by Al in both the roots and shoots but particularly in the shoots. The overexpression of ZmAT6 in maize and Arabidopsis plants increased their root growth and reduced the accumulation of Al, suggesting the contribution of ZmAT6 to Al tolerance. Moreover, the ZmAT6 transgenic maize plants had lower contents of malondialdehyde and reactive oxygen species (ROS), but much higher proline content and even lower Evans blue absorption in the roots compared with the wild type. Furthermore, the activity of several enzymes of the antioxidant system, such as peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX), increased in ZmAT6 transgenic maize plants, particularly SOD. Consistently, the expression of ZmSOD in transgenic maize was predominant upregulated by Al stress. Taken together, these findings revealed that ZmAT6 could at least partially confer enhanced tolerance to Al toxicity by scavenging ROS in maize.

Epigenetic Control of Plant Response to Heavy Metal Stress: A New View on Aluminum Tolerance

High concentrations of heavy metal (HM) ions impact agronomic staple crop production in acid soils (pH ≤ 5) due to their cytotoxic, genotoxic, and mutagenic effects. Among cytotoxic ions, the trivalent aluminum cation (Al³⁺) formed by solubilization of aluminum (Al) into acid soils, is one of the most abundant and toxic elements under acidic conditions. In recent years, several studies have elucidated the different signal transduction pathways involved in HM responses, identifying complementary genetic mechanisms conferring tolerance to plants. Although epigenetics has become more relevant in abiotic stress studies, epigenetic mechanisms underlying plant responses to HM stress remain poorly understood. This review describes the main epigenetic mechanisms related to crop responses during stress conditions, specifically, the molecular evidence showing how epigenetics is at the core of plant adaptation responses to HM ions. We highlight the epigenetic mechanisms that induce Al tolerance. Likewise, we analyze the pivotal relationship between epigenetic and genetic factors associated with HM tolerance. Finally, using rice as a study case, we performed a general analysis over previously whole-genome bisulfite-seq published data. Specific genes related to Al tolerance, measured in contrasting tolerant and susceptible rice varieties, exhibited differences in DNA methylation frequency. The differential methylation patterns could be associated with epigenetic regulation of rice responses to Al stress, highlighting the major role of epigenetics over specific abiotic stress responses.

OsIAGT1 Is a Glucosyltransferase Gene Involved in the Glucose Conjugation of Auxins in Rice

BACKGROUND

In cereal crop rice, auxin is known as an important class of plant hormone that regulates a plethora of plant growth and development. Glycosylation of auxin is known to be one of the important mechanisms mediating auxin homeostasis. However, the relevant auxin glucosyltransferase (GT) in rice still remains largely unknown.

RESULTS

In this study, using known auxin glucosyltransferases from other species as queries, twelve putative auxin UDP-glycosyltransferase (UGT) genes were cloned from rice and the one showing highest sequence similarity, named as OsIAGT1, was expressed as recombinant protein. In vitro enzymatic analysis showed that recombinant OsIAGT1 was capable of catalyzing glucosylation of IAA, IBA and other auxin analogs, and that OsIAGT1 is quite tolerant to a broad range of reaction conditions with peak activity at 30 °С and pH 8.0. OsIAGT1 showed favorite activity towards native auxins over artificially synthesized ones. Further study indicated that expression of OsIAGT1 can be upregulated by auxin in rice, and with OsIAGT1 overexpressing lines we confirmed that OsIAGT1 is indeed able to glucosylate IAA in vivo. Consistently, ectopic expression of OsIAGT1 leads to declined endogenous IAA content, as well as upregulated auxin synthesis genes and reduced expression of auxin-responsive genes, which likely leads to the reduced plant stature and root length in OsIAGT1 overexpression lines.

CONCLUSION

Our result indicated that OsIAGT1 plays an important role in mediating auxin homeostasis by catalyzing auxin glucosylation, and by which OsIAGT1 regulates growth and development in rice.

Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

BACKGROUND

The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice.

RESULTS

Genome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting's core collection constructed from 2262 Ting's collections with more than 3.8 million SNPs. Within Ting's core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance.

CONCLUSIONS

The present study provided important information for further using these elite genes existing in Ting's core collection for improvement of rice Al tolerance.

The functional identification of glycine-rich TtASR from Tetragonia tetragonoides (Pall.) Kuntze involving in plant abiotic stress tolerance

In this study, we reported on an ASR gene (TtASR) related to salt/drought tolerance from the edible halophyte Tetragonia tetragonoides (Pall.) Kuntze (Aizoaceae). A phylogenetic analysis revealed that TtASR was evolutionarily close to other two halophytic glycine-rich ASR members, SbASR-1 (from Salicornia brachiate) and SlASR (from Suaeda liaotungensis), with a typical abscisic acid (ABA)/water-deficit stress (WDS) domain at C-terminal. Quantitative RT-PCR analyses showed that TtASR was expressed in all tested different organs of the T. tetragonoides plant and that expression levels were apparently induced after salt, osmotic stress, and ABA treatments in T. tetragonoides seedlings. An induction of TtASR improved the growth performance of yeast and bacteria more than the control under high salinity, osmotic stress, and oxidative stress. TtASR was not a nuclear-specific protein in plant, and the transcriptional activation assay also demonstrated that TtASR could not activate reporter gene's expression in yeast. TtASR overexpressed Arabidopsis plants exhibited higher tolerance for salt/drought and oxidative stresses and lower ROS accumulation than wild type (WT) plants, accompanied by increased CAT, SOD activities, higher proline content, and lower MDA content in vivo. The results indicated that the TtASR was involved in plant responses to salt and drought, probably by mediating water homeostasis or by acting as ROS scavengers, and that it decreased the membrane damage and improved cellular osmotic adjustment that respond to abiotic stresses in microorganisms and plants.

PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana

Plant-growth-promoting rhizobacteria (PGPR) improve plant growth by altering the root architecture, although the mechanisms underlying this alteration have yet to be unravelled. Through microarray analysis of PGPR-treated rice roots, a large number of differentially regulated genes were identified. Ectopic expression of one of these genes, OsASR6 (ABA STRESS RIPENING6), had a remarkable effect on plant growth in Arabidopsis. Transgenic lines over-expressing OsASR6 had larger leaves, taller inflorescence bolts and greater numbers of siliques and seeds. The most prominent effect was observed in root growth, with the root biomass increasing four-fold compared with the shoot biomass increase of 1.7-fold. Transgenic OsASR6 over-expressing plants showed higher conductance, transpiration and photosynthesis rates, leading to an ˜30% higher seed yield compared with the control. Interestingly, OsASR6 expression led to alterations in the xylem structure, an increase in the xylem vessel size and altered lignification, which correlated with higher conductance. OsASR6 is activated by auxin and, in turn, increases auxin responses and root auxin sensitivity, as observed by the increased expression of auxin-responsive genes, such as SAUR32 and PINOID, and the key auxin transcription factor, ARF5. Collectively, these phenomena led to an increased root density. The effects of OsASR6 expression largely mimic the beneficial effects of PGPRs in rice, indicating that OsASR6 activation may be a key factor governing PGPR-mediated changes in rice. OsASR6 is a potential candidate for the manipulation of rice for improved productivity.

Transcriptome analysis reveals potential roles of a barley ASR gene that confers stress tolerance in transgenic rice

Control of gene expression and induction of cellular protection mechanisms are two important processes that plants employ to protect themselves against abiotic stresses. ABA-, stress, and ripening-induced (ASR) proteins have been identified to participate in such responses. Previous studies have proposed that these proteins can act as transcription factors and as molecular chaperones protecting transgenic plants against stresses; however a gene network regulated by ASRs has not been explored. To expand our knowledge on the function of these proteins in cereals, we present the functional characterization of a barley ASR gene. Expression of HvASR5 was almost ubiquitous in different organs and responded to ABA and to different stress treatments. When expressed ectopically, HvASR5 was able to confer drought and salt stress tolerance to Arabidopsis thaliana and to improve growth performance of rice plants under stress conditions. A transcriptomic analysis with two transgenic rice lines overexpressing HvASR5 helped to identify potential downstream targets and understand ASR-regulated cellular processes. HvASR5 up-regulated the expression of a distinct set of genes associated with stress responses, metabolic processes (particularly carbohydrate metabolism), as well as reproduction and development. These data, together with the confirmed nuclear and cytoplasmic localization of HvASR5, further support the hypothesis that HvASR5 can also carry out roles as molecular protector and transcriptional regulator.

Proteomic Profiling for Metabolic Pathways Involved in Interactive Effects of Elevated Carbon Dioxide and Nitrogen on Leaf Growth in a Perennial Grass Species

Elevated atmospheric CO₂ and nitrogen are major environmental factors affecting shoot growth. The objectives of this study are to determine the interactive effects of elevated CO₂ and nitrogen on leaf growth in tall fescue ( Festuca arundinacea) and to identify major proteins and associated metabolic pathways underlying CO₂-regulation of leaf growth under insufficient and sufficient nitrate conditions using proteomic analysis. Plants of tall fescue treated with low nitrate level (0.25 mM, LN), moderate nitrate level (4 mM, MN) and high nitrate level (32 mM, HN) were exposed to ambient (400 μmol mol^-1) and elevated (800 μmol mol^-1) CO₂ concentrations in environment-controlled growth chambers. Increased atmospheric CO₂ concentration increased leaf length and shoot biomass, which corresponded to increased content of indo-acetic acid, gibberellic acid, cytokinins and reduced content of abscisic acid under sufficient nitrate conditions (MN and HN conditions). Low nitrate supply limited shoot growth and hormonal responses to elevated CO₂. Proteomic analysis of plants exposed to elevated CO₂ under LN and MN conditions demonstrated the increases in the abundance of many proteins due to elevated CO₂ under MN condition involved with cell cycle and proliferation, transcription and translation, photosynthesis (ribosomal and chlorophyll a/b-binding proteins), amino acids synthesis, sucrose and starch metabolism, as well as ABA signaling pathways (ABA-induced proteins). Our results revealed major proteins and associated metabolic pathways associated with the interactive effects of elevated CO₂ and nitrate regulating leaf growth in a perennial grass species.

Molecular Mechanisms for Coping with Al Toxicity in Plants

Aluminum (Al) toxicity is one of the major constraints to agricultural production in acid soils. Molecular mechanisms of coping with Al toxicity have now been investigated in a range of plant species. Two main mechanisms of Al tolerance in plants are Al exclusion from the roots and the ability to tolerate Al in the roots. This review focuses on the recent discovery of novel genes and mechanisms that confer Al tolerance in plants and summarizes our understanding of the physiological, genetic, and molecular basis for plant Al tolerance. We hope this review will provide a theoretical basis for the genetic improvement of Al tolerance in plants.

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets

BACKGROUND

Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed.

METHODS

To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment.

RESULTS

We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr).

CONCLUSION

In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.

Aluminum Responsive Genes in Flax (Linum usitatissimum L.)

Flax (Linum usitatissimum L.) is a multipurpose crop which is used for the production of textile, oils, composite materials, pharmaceuticals, etc. Soil acidity results in a loss of seed and fiber production of flax, and aluminum toxicity is a major factor that depresses plant growth and development in acid conditions. In the present work, we evaluated gene expression alterations in four flax genotypes with diverse tolerance to aluminum exposure. Using RNA-Seq approach, we revealed genes that are differentially expressed under aluminum stress in resistant (Hermes, TMP1919) and sensitive (Lira, Orshanskiy) cultivars and selectively confirmed the identified alterations using qPCR. To search for differences in response to aluminum between resistant and sensitive genotypes, we developed the scoring that allowed us to suggest the involvement of MADS-box and NAC transcription factors regulating plant growth and development and enzymes participating in cell wall modifications in aluminum tolerance in flax. Using Gene Ontology (GO) enrichment analysis, we revealed that glutathione metabolism, oxidoreductase, and transmembrane transporter activities are the most affected by the studied stress in flax. Thus, we identified genes that are involved in aluminum response in resistant and sensitive genotypes and suggested genes that contribute to flax tolerance to the aluminum stress.

Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels; thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., “Terpenoid backbone biosynthesis”, “Ribosome”, “Amino sugar and nucleotide sugar metabolism”, “Plant hormone signal transduction”, “TCA cycle”, “Synthesis and degradation of ketone bodies”, and “Butanoate metabolism” were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., “Sulfur metabolism”) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in “Starch and sucrose metabolism”, “Metabolic pathway”, and “Amino sugar and nucleotide sugar metabolism”.

Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize

In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants.

A stress-associated protein, LmSAP, from the halophyte Lobularia maritima provides tolerance to heavy metals in tobacco through increased ROS scavenging and metal detoxification processes

Agricultural soil pollution by heavy metals is a severe global ecological problem. We recently showed that overexpression of LmSAP, a member of the stress-associated protein (SAP) gene family isolated from Lobularia maritima, in transgenic tobacco led to enhanced tolerance to abiotic stress. In this study, we characterised the response of LmSAP transgenic tobacco plants to metal stresses (cadmium (Cd), copper (Cu), manganese (Mn), and zinc (Zn)). In L. maritima, LmSAP expression increased after 12 h of treatment with these metals, suggesting its involvement in the plant response to heavy metal stress. LmSAP transgenic tobacco plants subjected to these stress conditions were healthy, experienced higher seedling survival rates, and had longer roots than non-transgenic plants (NT). However, they exhibited higher tolerance towards cadmium and manganese than towards copper and zinc. LmSAP-overexpressing tobacco seedlings accumulated more cadmium, copper, and manganese compared with NT plants, but displayed markedly decreased hydrogen peroxide (H2O2) and lipid peroxidation levels after metal treatment. Activities of the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) were significantly higher in transgenic plants than in NT plants after exposure to metal stress. LmSAP overexpression also enhanced the transcription of several genes encoding metallothioneins (Met1, Met2, Met3, Met4, and Met5), a copper transport protein CCH, a Cys and His-rich domain-containing protein RAR1 (Rar1), and a ubiquitin-like protein 5 (PUB1), which are involved in metal tolerance in tobacco. Our findings indicate that LmSAP overexpression in tobacco enhanced tolerance to heavy metal stress by protecting the plant cells against oxidative stress, scavenging reactive oxygen species (ROS), and decreasing the intracellular concentration of free heavy metals through its effect on metal-binding proteins in the cytosol.

Emerging Pleiotropic Mechanisms Underlying Aluminum Resistance and Phosphorus Acquisition on Acidic Soils

Aluminum (Al) toxicity on acidic soils significantly damages plant roots and inhibits root growth. Hence, crops intoxicated by Al become more sensitive to drought stress and mineral nutrient deficiencies, particularly phosphorus (P) deficiency, which is highly unavailable on tropical soils. Advances in our understanding of the physiological and genetic mechanisms that govern plant Al resistance have led to the identification of Al resistance genes, both in model systems and in crop species. It has long been known that Al resistance has a beneficial effect on crop adaptation to acidic soils. This positive effect happens because the root systems of Al resistant plants show better development in the presence of soil ionic Al3+ and are, consequently, more efficient in absorbing sub-soil water and mineral nutrients. This effect of Al resistance on crop production, by itself, warrants intensified efforts to develop and implement, on a breeding scale, modern selection strategies to profit from the knowledge of the molecular determinants of plant Al resistance. Recent studies now suggest that Al resistance can exert pleiotropic effects on P acquisition, potentially expanding the role of Al resistance on crop adaptation to acidic soils. This appears to occur via both organic acid (OA)- and non-OA transporters governing a joint, iron-dependent interplay between Al resistance and enhanced P uptake, via changes in root system architecture. Current research suggests this interplay to be part of a P stress response, suggesting that this mechanism could have evolved in crop species to improve adaptation to acidic soils. Should this pleiotropism prove functional in crop species grown on acidic soils, molecular breeding based on Al resistance genes may have a much broader impact on crop performance than previously anticipated. To explore this possibility, here we review the components of this putative effect of Al resistance genes on P stress responses and P nutrition to provide the foundation necessary to discuss the recent evidence suggesting pleiotropy as a genetic linkage between Al resistance and P efficiency. We conclude by exploring what may be needed to enhance the utilization of Al resistance genes to improve crop production on acidic soils.

Ipomoea pes-caprae IpASR Improves Salinity and Drought Tolerance in Transgenic Escherichia coli and Arabidopsis

Ipomoea pes-caprae L. is an extremophile halophyte with strong adaptability to seawater and drought. It is widely used in the ecological restoration of coastal areas or degraded islands in tropical and subtropical regions. In this study, a new abscisic acid, stressandripening (ASR) gene, IpASR, was reported, and is mainly associated with biological functions involved in salt and drought tolerance. Sequence analysis of IpASR showed that this protein contains an ABA/WDS (abscisic acid/water deficit stress) domain, which is a common feature of all plant ASR members. Overexpression of IpASR improved Escherichia coli growth performance compared with the control under abiotic stress treatment. The transgenic overexpressing IpASR Arabidopsis showed higher tolerance to salt and drought stress than the wild type and lower accumulation of hydrogen peroxide (H₂O₂) and superoxide (O₂⁻) accompanied by increased antioxidant enzyme activity in vivo. IpASR exhibits transcription factor’s activity. Therefore, the overexpression of IpASR in Arabidopsis is supposed to influence the expression of some genes involved in anti-oxidative and abiotic stresses. The results indicate that IpASR is involved in the plant response to salt and drought and probably acts as a reactive oxygen species scavenger or transcription factor, and therefore influences physiological processes associated with various abiotic stresses in plants.

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.

Expression patterns and promoter analyses of aluminum-responsive NAC genes suggest a possible growth regulation of rice mediated by aluminum, hormones and NAC transcription factors

In acid soils, the solubilized form of aluminum, Al+3, decreases root growth and affects the development of most crops. However, like other toxic elements, Al can have hormetic effects on plant metabolism. Rice (Oryza sativa) is one of the most tolerant species to Al toxicity, and when this element is supplied at low doses, growth stimulation has been observed, which could be due to combined mechanisms that are partly triggered by NAC transcription factors. This protein family can regulate vital processes in plants, including growth, development, and response to environmental stimuli, whether biotic or abiotic. Under our experimental conditions, 200 μM Al stimulated root growth and the formation of tillers; it also caused differential expression of a set of NAC genes. The promoter regions of the genes regulated by Al were analyzed and the cis-acting elements that are potentially involved in the responses to different stimuli, including environmental stress, were identified. Through the Genevestigator platform, data on the expression of NAC genes were obtained by experimental condition, tissue, and vegetative stage. This is the first study on NAC genes where in vivo and in silico data are complementarily analyzed, relating the hormetic effect of Al on plant growth and gene expression with a possible interaction in the response to phytohormones in rice. These findings could help to elucidate the possible convergence between the signaling pathways mediated by phytohormones and the role of the NAC transcription factors in the regulation of growth mediated by low Al doses.

Overexpression of a peroxidase gene (AtPrx64) of Arabidopsis thaliana in tobacco improves plant's tolerance to aluminum stress

KEY MESSAGE

AtPrx64 is one of the peroxidases gene up-regulated in Al stress and has some functions in the formation of plant second cell wall. Its overexpression may improve plant tolerance to Al by some ways. Studies on its function under Al stress may help us to understand the mechanism of plant tolerance to Al stress. In Arabidopsis thaliana, the expressions of some genes (AtPrxs) encoding class III plant peroxidases have been found to be either up-regulated or down-regulated under aluminum (Al) stress. Among 73 genes that encode AtPrxs in Arabidopsis, AtPrx64 is always up-regulated by Al stress, suggesting this gene plays protective roles in response to such stress. In this study, transgenic tobacco plants were generated to examine the effects of overexpressing of AtPrx64 gene on the tolerance to Al stress. The results showed that overexpression of AtPrx64 gene increased the root growth and reduced the accumulation of Al and ROS in the roots. Compared with wild type controls, transgenic tobaccos had much less soluble proteins and malondialdehyde in roots and much more root citrate exudation. The activity of plasma membrane (PM) H+-ATPase, the phosphorylation of PM H+-ATPase and its interaction with 14-3-3 proteins increased in transgenic tobaccos; moreover, the content of lignin in root tips also increased. Taken together, these results showed that overexpression of AtPrx64 gene might enhance the tolerance of tobacco to Al stress.

Transcriptome Analysis of Al-Induced Genes in Buckwheat (Fagopyrum esculentum Moench) Root Apex: New Insight into Al Toxicity and Resistance Mechanisms in an Al Accumulating Species

Relying on Al-activated root oxalate secretion, and internal detoxification and accumulation of Al, buckwheat is highly Al resistant. However, the molecular mechanisms responsible for these processes are still poorly understood. It is well-known that root apex is the critical region of Al toxicity that rapidly impairs a series of events, thus, resulting in inhibition of root elongation. Here, we carried out transcriptome analysis of the buckwheat root apex (0-1 cm) with regards to early response (first 6 h) to Al stress (20 μM), which is crucial for identification of both genes and processes involved in Al toxicity and tolerance mechanisms. We obtained 34,469 unigenes with 26,664 unigenes annotated in the NCBI database, and identified 589 up-regulated and 255 down-regulated differentially expressed genes (DEGs) under Al stress. Functional category analysis revealed that biological processes differ between up- and down-regulated genes, although 'metabolic processes' were the most affected category in both up- and down-regulated DEGs. Based on the data, it is proposed that Al stress affects a variety of biological processes that collectively contributes to the inhibition of root elongation. We identified 30 transporter genes and 27 transcription factor (TF) genes induced by Al. Gene homology analysis highlighted candidate genes encoding transporters associated with Al uptake, transport, detoxification, and accumulation. We also found that TFs play critical role in transcriptional regulation of Al resistance genes in buckwheat. In addition, gene duplication events are very common in the buckwheat genome, suggesting a possible role for gene duplication in the species' high Al resistance. Taken together, the transcriptomic analysis of buckwheat root apex shed light on the processes that contribute to the inhibition of root elongation. Furthermore, the comprehensive analysis of both transporter genes and TF genes not only deep our understanding on the responses of buckwheat roots to Al toxicity but provide a good start for functional characterization of genes critical for Al tolerance.

Aluminum Enhances Growth and Sugar Concentration, Alters Macronutrient Status and Regulates the Expression of NAC Transcription Factors in Rice

Aluminum (Al) is a beneficial element for some plant species, especially when used at low concentrations. Though some transcription factors are induced by exposure to this element, no data indicate that Al regulates the expression of NAC genes in rice. In this study we tested the effect of applying 200 μM Al on growth, chlorophyll, amino acids, sugars, macronutrient concentration and regulation of NAC transcription factors gene expression in 24-day-old plants of four rice (Oryza sativa ssp. indica) cultivars: Cotaxtla, Tres Ríos, Huimanguillo and Temporalero, grown hydroponically under greenhouse conditions. Twenty days after treatment, we observed that Al enhanced growth in the four cultivars studied. On average, plants grown in the presence of Al produced 140% more root dry biomass and were 30% taller than control plants. Cotaxtla and Temporalero showed double the root length, while Huimanguillo and Cotaxtla had three times more root fresh biomass and 2.5 times more root dry biomass. Huimanguillo plants showed 1.5 times more shoot height, while Cotaxtla had almost double the root dry biomass. With the exception of Tres Ríos, the rest of the cultivars had almost double the chlorophyll concentration when treated with Al, whereas amino acid and proline concentrations were not affected by Al. Sugar concentration was also increased in plants treated with Al, almost 11-fold in comparison to the control. Furthermore, we observed a synergic response of Al application on P and K concentration in roots, and on Mg concentration in shoots. Twenty-four hours after Al treatment, NAC transcription factors gene expression was measured in roots by quantitative RT-PCR. Of the 57 NAC transcription factors genes primer-pairs tested, we could distinguish that 44% (25 genes) showed different expression patterns among rice cultivars, with most of the genes induced in Cotaxtla and Temporalero plants. Of the 25 transcription factors up-regulated, those showing differential expression mostly belonged to the NAM subfamily (56%). We conclude that Al improves growth, increases sugar concentration, P and K concentrations in roots, and Mg concentration in shoots, and report, for the first time, that Al differentially regulates the expression of NAC transcription factors in rice.

Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces

Trivalent aluminum (Al³⁺) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting's rice core collection). Our results showed that the Ting's rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait-marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R²) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding.