Physiological and molecular characterization of aluminum resistance in Medicago truncatula

Genome-wide analysis and identification of microRNAs in Medicago truncatula under aluminum stress

Numerous studies have shown that plant microRNAs (miRNAs) play key roles in plant growth and development, as well as in response to biotic and abiotic stresses; however, the role of miRNA in legumes under aluminum (Al) stress have rarely been reported. Therefore, here, we aimed to investigate the role of miRNAs in and their mechanism of Al tolerance in legumes. To this end, we sequenced a 12-strand-specific library of Medicago truncatula under Al stress. A total of 195.80 M clean reads were obtained, and 876 miRNAs were identified, of which, 673 were known miRNAs and 203 were unknown. A total of 55 miRNAs and their corresponding 2,502 target genes were differentially expressed at various time points during Al stress. Further analysis revealed that mtr-miR156g-3p was the only miRNA that was significantly upregulated at all time points under Al stress and could directly regulate the expression of genes associated with root cell growth. Three miRNAs, novel_miR_135, novel_miR_182, and novel_miR_36, simultaneously regulated the expression of four Al-tolerant transcription factors, GRAS, MYB, WRKY, and bHLH, at an early stage of Al stress, indicating a response to Al stress. In addition, legume-specific miR2119 and miR5213 were involved in the tolerance mechanism to Al stress by regulating F-box proteins that have protective effects against stress. Our results contribute to an improved understanding of the role of miRNAs in Al stress in legumes and provide a basis for studying the molecular mechanisms of Al stress regulation.

Identification of two chickpea multidrug and toxic compound extrusion transporter genes transcriptionally upregulated upon aluminum treatment in root tips

Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al³⁺) and Al treatments (15, 30 μM Al³⁺). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea MATE genes (CaMATE1-4) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula. Transcriptome data showed that CaMATE1-4 have diverse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root. Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic diversity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al³⁺ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.

Elshikh M, Jamil A, Nasir JA, Dvořáčková H, Dvořáček J. Genome-wide analysis of sucrose synthase family in soybean and their expression in response to abiotic stress and seed development

The sucrose synthase (SS) is an important enzyme family which play a vital role in sugar metabolism to improve the fruit quality of the plants. In many plant species, the members of SS family have been investigated but the detailed information is not available in legumes particularly and Glycine max specifically. In the present study, we found thirteen SS members (GmSS1-GmSS13) in G. max genome. High conserved regions were present in the GmSS sequences that may due to the selection pressure during evolutionary events. The segmental duplication was the major factor to increase the number of GmSS family members. The identified thirteen GmSS genes were divided into Class I, Class II and Class III with variable numbers of genes in each class. The protein interaction of GmSS gave the co-expression of sucrose synthase with glucose-1-phosphate adenylyltransferase while SLAC and REL test found number of positive sites in the coding sequences of SS family members. All the GmSS family members except GmSS7 and few of class III members, were highly expressed in all the soybean tissues. The expression of the class I members decreased during seed development, whireas, the class II members expression increased during the seed developing, may involve in sugar metabolism during seed development. Solexa sequencing libraries of acidic condition (pH 4.2) stress samples showed that the expression of class I GmSS genes increased 1- to 2-folds in treated samples than control. The differential expression pattern was observed between the members of a paralogous. This study provides detailed genome-wide analysis of GmSS family in soybean that will provide new insights for future evolutionary and soybean breeding to improve the plant growth and development.

Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L

Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level. Phylogenetic analysis classified them into four subfamilies comprising 11 subgroups. Generally, five kinds of motifs were found in group G1, and most were located at the N-terminus, which might confer these genes with Al detoxification functions. Furthermore, 10 putative Al detoxification-related MsMATE genes were identified and the expression of five genes was significantly increased after Al treatment, indicating that these genes might play important roles in conferring Al tolerance to alfalfa. Considering the limited functional understanding of MATE transcripts in alfalfa, our findings will be valuable for the functional investigation and application of this family in alfalfa.

Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus

Ionic aluminum (Al) in acidic soils, comprising approximately 50% of arable land globally, is highly toxic to most plant species. Populus grow naturally in acidic soils and tolerate high concentrations of Al. Multidrug and toxic compound extrusion (MATE) family genes in plants are involved in responses to Al tolerance. To date, however, the functional roles of the MATE genes in Populus remain unclear. In the present study, 71 putative MATE transporters were predicted in the genome of Populus trichocarpa. The chromosome distribution, phylogenetic relationships, and expression level analysis revealed that four candidate MATE genes belonging to subgroup IIIc might contribute to high Al tolerance in poplar. Further, the expression levels of two subgroup IIIc members, PtrMATE1 and PtrMATE2, were induced by Al stress. Transient expression in onion epidermal cells showed that PtrMATE1 was localized to the plasma membrane. Overexpression of PtrMATE1 increased Al-induced secretion of citrate from the root apex of transgenic plants. Al-induced inhibition of root growths were alleviated in both PtrMATE1 overexpression lines in Populus and in Arabidopsis compared with wild-type plants. In addition, PtrMATE1 expression was induced at 12 h after exposure to Al stress whereas PtrMATE2 expression was induced at 24 h, indicating that these proteins coordinately function in response to Al stress in poplar. Taken together, these results provide important insights into the molecular mechanisms involved in Al tolerance in poplar.

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.

Cyclopiazonic Acid Is a Pathogenicity Factor for Aspergillus flavus and a Promising Target for Screening Germplasm for Ear Rot Resistance

Aspergillus flavus, an opportunistic pathogen, contaminates maize and other key crops with carcinogenic aflatoxins (AFs). Besides AFs, A. flavus makes many more secondary metabolites (SMs) whose toxicity in insects or vertebrates has been studied. However, the role of SMs in the invasion of plant hosts by A. flavus remains to be investigated. Cyclopiazonic acid (CPA), a neurotoxic SM made by A. flavus, is a nanomolar inhibitor of endoplasmic reticulum calcium ATPases (ECAs) and a potent inducer of cell death in plants. We hypothesized that CPA, by virtue of its cytotoxicity, may serve as a key pathogenicity factor that kills plant cells and supports the saprophytic life style of the fungus while compromising the host defense response. This proposal was tested by two complementary approaches. A comparison of CPA levels among A. flavus isolates indicated that CPA may be a determinant of niche adaptation, i.e., isolates that colonize maize make more CPA than those restricted only to the soil. Further, mutants in the CPA biosynthetic pathway are less virulent in causing ear rot than their wild-type parent in field inoculation assays. Additionally, genes encoding ECAs are expressed in developing maize seeds and are induced by A. flavus infection. Building on these results, we developed a seedling assay in which maize roots were exposed to CPA, and cell death was measured as Evans Blue uptake. Among >40 maize inbreds screened for CPA tolerance, inbreds with proven susceptibility to ear rot were also highly CPA sensitive. The publicly available data on resistance to silk colonization or AF contamination for many of the lines was also broadly correlated with their CPA sensitivity. In summary, our studies show that i) CPA serves as a key pathogenicity factor that enables the saprophytic life style of A. flavus and ii) maize inbreds are diverse in their tolerance to CPA. Taking advantage of this natural variation, we are currently pursuing both genome-wide and candidate gene approaches to identify novel components of maize resistance to Aspergillus ear rot.

Diverse functions of multidrug and toxin extrusion (MATE) transporters in citric acid efflux and metal homeostasis in Medicago truncatula

The multidrug and toxin extrusion (MATE) transporter family comprises 70 members in the Medicago truncatula genome, and they play seemingly important, yet mostly uncharacterized, physiological functions. Here, we employed bioinformatics and molecular genetics to identify and characterize MATE transporters involved in citric acid export, Al³⁺ tolerance and Fe translocation. MtMATE69 is a citric acid transporter induced by Fe-deficiency. Overexpression of MtMATE69 in hairy roots altered Fe homeostasis and hormone levels under Fe-deficient or Fe-oversupplied conditions. MtMATE66 is a plasma membrane citric acid transporter primarily expressed in root epidermal cells. The mtmate66 mutant had less root growth than the wild type under Al³⁺ stress, and seedlings were chlorotic under Fe-deficient conditions. Overexpression of MtMATE66 rendered hairy roots more tolerant to Al³⁺ toxicity. MtMATE55 is involved in seedling development and iron homeostasis, as well as hormone signaling. The mtmate55 mutant had delayed development and chlorotic leaves in mature plants. Both knock-out and overexpression mutants of MtMATE55 showed altered Fe accumulation and abnormal hormone levels compared with the wild type. We demonstrate that the zinc-finger transcription factor MtSTOP is essentially required for MtMATE66 expression and plant resistance to H⁺ and Al³⁺ toxicity. The proper expression of two previously characterized MATE flavonoid transporters MtMATE1 and MtMATE2 also depends on several transcription factors. This study reveals not only functional diversity of MATE transporters and regulatory mechanisms in legumes against H⁺ and Al³⁺ stresses, but also casts light on their role in metal nutrition and hormone signaling under various stresses.

Screening of faba bean (Vicia faba L.) accessions to acidity and aluminium stresses

Background

Faba bean is an important starch-based protein crop produced worldwide. Soil acidity and aluminium toxicity are major abiotic stresses affecting its production, so in regions where soil acidity is a problem, there is a gap between the potential and actual productivity of the crop. Hence, we set out to evaluate acidity and aluminium tolerance in a range of faba bean germplasm using solution culture and pot experiments.

Methods

A set of 30 accessions was collected from regions where acidity and aluminium are or are not problems. The accessions were grown in solution culture and a subset of 10 was grown first in peat and later in perlite potting media. In solution culture, morphological parameters including taproot length, root regrowth and root tolerance index were measured, and in the pot experiments the key measurements were taproot length, plant biomass, chlorophyll concentration and stomatal conductance.

Result

Responses to acidity and aluminium were apparently independent. Accessions Dosha and NC 58 were tolerant to both stress. Kassa and GLA 1103 were tolerant to acidity showing less than 3% reduction in taproot length. Aurora and Messay were tolerant to aluminium. Babylon was sensitive to both, with up to 40% reduction in taproot length from acidity and no detectable recovery from Al³⁺ challenge.

Discussion

The apparent independence of the responses to acidity and aluminium is in agreement with the previous research findings, suggesting that crop accessions separately adapt to H⁺ and Al³⁺ toxicity as a result of the difference in the nature of soil parent materials where the accession originated. Differences in rankings between experiments were minor and attributable to heterogeneity of seed materials and the specific responses of accessions to the rooting media. Use of perlite as a potting medium offers an ideal combination of throughput, inertness of support medium, access to leaves for detection of their stress responses, and harvest of clean roots for evaluation of their growth.

Responses of symbiotic nitrogen-fixing common bean to aluminum toxicity and delineation of nodule responsive microRNAs

Aluminum (Al) toxicity is widespread in acidic soils where the common bean (Phaseolus vulgaris), the most important legume for human consumption, is produced and it is a limiting factor for crop production and symbiotic nitrogen fixation. We characterized the nodule responses of common bean plants inoculated with Rhizobioum tropici CIAT899 and the root responses of nitrate-fertilized plants exposed to excess Al in low pH, for long or short periods. A 43-50% reduction in nitrogenase activity indicates that Al toxicity (Alt) highly affected nitrogen fixation in common bean. Bean roots and nodules showed characteristic symptoms for Alt. In mature nodules Al accumulation and lipoperoxidation were observed in the infected zone, while callose deposition and cell death occurred mainly in the nodule cortex. Regulatory mechanisms of plant responses to metal toxicity involve microRNAs (miRNAs) along other regulators. Using a miRNA-macroarray hybridization approach we identified 28 (14 up-regulated) Alt nodule-responsive miRNAs. We validated (quantitative reverse transcriptase-PCR) the expression of eight nodule responsive miRNAs in roots and in nodules exposed to high Al for long or short periods. The inverse correlation between the target and miRNA expression ratio (stress:control) was observed in every case. Generally, miRNAs showed a higher earlier response in roots than in nodules. Some of the common bean Alt-responsive miRNAs identified has also been reported as differentially expressed in other plant species subjected to similar stress condition. miRNA/target nodes analyzed in this work are known to be involved in relevant signaling pathways, thus we propose that the participation of miR164/NAC1 (NAM/ATAF/CUC transcription factor) and miR393/TIR1 (TRANSPORT INHIBITOR RESPONSE 1-like protein) in auxin and of miR170/SCL (SCARECROW-like protein transcription factor) in gibberellin signaling is relevant for common bean response/adaptation to Al stress. Our data provide a foundation for evaluating the individual roles of miRNAs in the response of common bean nodules to Alt.

Plant chitinase responses to different metal-type stresses reveal specificity

KEY MESSAGE

Chitinases in Glycine max roots specifically respond to different metal types and reveal a polymorphism that coincides with sensitivity to metal toxicity. Plants evolved various defense mechanisms to cope with metal toxicity. Chitinases (EC 3.2.1.14), belonging to so-called pathogenesis-related proteins, act as possible second line defense compounds in plants exposed to metals. In this work their activity was studied and compared in two selected soybean (Glycine max L.) cultivars, the metal-tolerant cv. Chernyatka and the sensitive cv. Kyivska 98. Roots were exposed to different metal(loid)s such as cadmium, arsenic and aluminum that are expected to cause toxicity in different ways. For comparison, a non-metal, NaCl, was applied as well. The results showed that the sensitivity of roots to different stressors coincides with the responsiveness of chitinases in total protein extracts. Moreover, detailed analyses of acidic and neutral proteins identified one polymorphic chitinase isoform that distinguishes between the two cultivars studied. This isoform was stress responsive and thus could reflect the evolutionary adaptation of soybean to environmental cues. Activities of the individual chitinases were dependent on metal type as well as the cultivar pointing to their more complex role in plant defense during this type of stress.

Influence of arbuscular mycorrhizal colonisation on cadmium induced Medicago truncatula root isoflavonoid accumulation

Cadmium is a serious environmental pollution threats to the planet. Its accumulation in plants affects many cellular functions, resulting in growth and development inhibition, whose mechanisms are not fully understood. However, some fungi forming arbuscular mycorrhizal symbiosis with the majority of plant species have the capacity to buffer the deleterious effect of this heavy metal. In the present work we investigated the capacity of Rhizophagus irregularis (syn. Glomus irregularis) to alleviate cadmium stress in Medicago truncatula. In spite of a reduction in all mycorrhizal parameters, plants colonized for 21 days by R. irregularis and treated by 2 mg kg⁻¹ cadmium displayed less growth inhibition in comparison to plants grown without cadmium. Cadmium strongly increased the accumulation of some isoflavonoids and their derivates: formononetin, malonylononin, medicarpin 3-O-β-(6'-malonylglucoside), medicarpin and coumestrol. Interestingly, in plants colonized by R. irregularis we noticed a strong reduction of the cadmium-induced accumulation of root isoflavonoids, a part for medicarpin and coumestrol. Moreover, transcripts of chalcone reductase, a protein that we reported previously as being down-regulated in R. irregularis-colonized M. truncatula roots, revealed a similar expression pattern with a strong increase in response to cadmium and a reduced expression in cadmium-treated mycorrhizal roots.

Comparative genome-wide transcriptional analysis of Al-responsive genes reveals novel Al tolerance mechanisms in rice

Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 µM AlCl(3) for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.

Mechanisms of magnesium amelioration of aluminum toxicity in soybean at the gene expression level

Micromolar concentration of magnesium (Mg) in culture solution is known to ameliorate aluminum (Al) toxicity in soybean and other leguminous species. To advance the understanding of this phenomenon at the level of gene expression in soybean, we undertook a comparative transcriptome analysis using DNA microarrays and Al-tolerant and Al-sensitive genotypes treated with Al ions alone or Al plus Mg ions. We observed a more rapid alteration of transcription for Al-tolerant than Al-sensitive soybean after introduction of Mg into Al-containing medium, but at 72 h, far more genes were altered (both upregulated and downregulated) in the Al-sensitive line, reflecting the known greater saving effect of Mg for Al-sensitive than Al-tolerant lines. Mg appears to ameliorate Al toxicity in the sensitive genotype by the dual mechanisms of (i) specifically increasing the expression level of several genes that are upregulated in the Al-treated, Al-tolerant genotype in the absence of Mg and (ii) possibly saving energy by decreasing expression of most genes relative to expression under Al stress. Mg-mediated reduction in gene expression also appears to be an important mechanism of Mg protection of the Al-tolerant genotype.

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)

BACKGROUND

Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth.

RESULTS

Treatment of the aspen roots with 500 μM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE.

CONCLUSION

Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.

The role of the root apoplast in aluminium-induced inhibition of root elongation and in aluminium resistance of plants: a review

BACKGROUND

Aluminium (Al) toxicity is the most important soil constraint for plant growth and development in acid soils. The mechanism of Al-induced inhibition of root elongation is still not well understood, and it is a matter of debate whether the primary lesions of Al toxicity are apoplastic or symplastic.

SCOPE

The present review focuses on the role of the apoplast in Al toxicity and resistance, summarizing evidence from our own experimental work and other evidence published since 1995.

CONCLUSIONS

The binding of Al in the cell wall particularly to the pectic matrix and to the apoplastic face of the plasma membrane in the most Al-sensitive root zone of the root apex thus impairing apoplastic and symplastic cell functions is a major factor leading to Al-induced inhibition of root elongation. Although symplastic lesions of Al toxicity cannot be excluded, the protection of the root apoplast appears to be a prerequisite for Al resistance in both Al-tolerant and Al-accumulating plant species. In many plant species the release of organic acid anions complexing Al, thus protecting the root apoplast from Al binding, is a most important Al resistance mechanism. However, there is increasing physiological, biochemical and, most recently also, molecular evidence showing that the modification of the binding properties of the root apoplast contributes to Al resistance. A further in-depth characterization of the Al-induced apoplastic reaction in the most Al-sensitive zone of the root apex is urgently required, particularly to understand the Al resistance of the most Al-resistant plant species.

Identification of rice Al-responsive genes by semi-quantitative polymerase chain reaction using sulfite reductase as a novel endogenous control

Based on the evidence that Al resistance is an inducible process and rice is an Al-resistant crop, identification of Al-responsive genes from rice may help to further clone Al-resistant genes in plants. Semi-quantitative and real-time polymerase chain reaction (PCR) is widely applied in gene transcriptional analyses, particularly for those genes with low transcript abundance. Normalization with proper endogenous control (EC) genes is critical for these two approaches in terms of reliability and precision. We first noticed that the expression of several commonly-used EC genes was depressed under Al stress, while sulfite reductase gene (SR) was stable throughout the Al treatment. The reliability of SR as an EC gene was further tested by analyzing the expression of a number of genes in response to Al challenge. Except for the consistent results obtained for the four previously-identified genes, nine additional genes were newly defined as Al-responsive in this study. Collectively, our results suggest that SR can be used as a novel EC gene for semi-quantitative and real-time PCR analysis of Al responsive genes, and that activated transport of silicon and stimulated metabolism of carotenoid and terpenoid could be involved in Al resistance in rice plants.

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress

BACKGROUND

The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10 degrees C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach.

RESULTS

Regulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10 degrees C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters.Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2 spikes within the initial 6 to 12 hours. Oxidative-independent responses involve DREB/CBF, RAP2 and RAV1 factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters.

CONCLUSION

Genome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries.

Identification of Aluminum Responsive Genes in Al-Tolerant Soybean Line PI 416937

Soybean is one of the most aluminum (Al) sensitive plants. The complex inheritance of Al tolerance trait has so far undermined breeding efforts to develop Al-tolerant soybeans. Discovering the genetic factors underlying the Al tolerance mechanisms would undoubtedly accelerate the pace of such endeavor. As a first step toward this goal, we analyzed the transcriptome profile in roots of Al-tolerant soybean line PI 416937 comparing Al-treated and untreated control plants using DNA microarrays. Many genes involved in transcription activation, stress response, cell metabolism and signaling were differentially expressed. Patterns of gene expression and mechanisms of Al toxicity and tolerance suggest that Cys2His2 and ADR6 transcription activators, cell wall modifying enzymes, and phytosulfokines growth factor play role in soybean Al tolerance. Our data provide insights into the molecular mechanisms of soybean Al tolerance and will have practical value in genetic improvement of Al tolerance trait.

Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in Arabidopsis thaliana

BACKGROUND

Rhizotoxic ions in problem soils inhibit nutrient and water acquisition by roots, which in turn leads to reduced crop yields. Previous studies on the effects of rhizotoxic ions on root growth and physiological functions suggested that some mechanisms were common to all rhizotoxins, while others were more specific. To understand this complex system, we performed comparative transcriptomic analysis with various rhizotoxic ions, followed by bioinformatics analysis, in the model plant Arabidopsis thaliana.

RESULTS

Roots of Arabidopsis were treated with the major rhizotoxic stressors, aluminum (Al) ions, cadmium (Cd) ions, copper (Cu) ions and sodium (NaCl) chloride, and the gene expression responses were analyzed by DNA array technology. The top 2.5% of genes whose expression was most increased by each stressor were compared with identify common and specific gene expression responses induced by these stressors. A number of genes encoding glutathione-S-transferases, peroxidases, Ca-binding proteins and a trehalose-synthesizing enzyme were induced by all stressors. In contrast, gene ontological categorization identified sets of genes uniquely induced by each stressor, with distinct patterns of biological processes and molecular function. These contained known resistance genes for each stressor, such as AtALMT1 (encoding Al-activated malate transporter) in the Al-specific group and DREB (encoding dehydration responsive element binding protein) in the NaCl-specific group. These gene groups are likely to reflect the common and differential cellular responses and the induction of defense systems in response to each ion. We also identified co-expressed gene groups specific to rhizotoxic ions, which might aid further detailed investigation of the response mechanisms.

CONCLUSION

In order to understand the complex responses of roots to rhizotoxic ions, we performed comparative transcriptomic analysis followed by bioinformatics characterization. Our analyses revealed that both general and specific genes were induced in Arabidopsis roots exposed to various rhizotoxic ions. Several defense systems, such as the production of reactive oxygen species and disturbance of Ca homeostasis, were triggered by all stressors, while specific defense genes were also induced by individual stressors. Similar studies in different plant species could help to clarify the resistance mechanisms at the molecular level to provide information that can be utilized for marker-assisted selection.