Spatial transcriptomes of iron-deficient and cadmium-stressed rice

Kitchen compost-derived humic acid application promotes ryegrass growth and enhances the accumulation of Cd: An analysis of the soil microenvironment and rhizosphere functional microbes

Phytoremediation is an environmentally friendly and safe approach for remediating environments contaminated with heavy metals. Humic acid (HA) has high biological activity and can effectively complex with heavy metals. However, whether HA affects available Cd storage and the Cd accumulation ability of plants by altering the soil microenvironment and the distribution of special functional microorganisms remains unclear. Here, we investigated the effects of applying kitchen compost-derived HA on the growth and Cd enrichment capacity of ryegrass (Lolium perenne L.). Additionally, the key role of HA in regulating the structure of rhizosphere soil bacterial communities was identified. HA promoted the growth of perennial ryegrass and biomass accumulation and enhanced the Cd enrichment capacity of ryegrass. The positive effect of HA on the soil microenvironment and rhizosphere bacterial community was the main factor promoting the growth of ryegrass, and this was confirmed by the significant positive correlation between the ryegrass growth index and the content of SOM, AP, AK, and AN, as well as the abundance of rhizosphere growth-promoting bacteria such as Pseudomonas, Steroidobacter, Phenylobacterium, and Caulobacter. HA passivated Cd and inhibited the translocation capacity of ryegrass. The auxiliary effect of resistant bacteria on plants drove the absorption of Cd by ryegrass. In addition, HA enhanced the remediation of Cd-contaminated soil by ryegrass under different Cd levels, which indicated that kitchen compost-derived HA could be widely used for the phytoremediation of Cd-contaminated soil. Generally, our findings will aid the development of improved approaches for the use of kitchen compost-derived HA for the remediation of Cd-contaminated soil.

Cross talk between Cu excess and Fe deficiency in the roots of rice

Copper (Cu) and iron (Fe) share similar characteristics and participate as coenzymes in several physiological processes. Both Cu excess and Fe deficiency result in chlorosis, however, the crosstalk between the two is not clear in rice. In this study, we performed transcriptome analysis for Cu excess and Fe deficiency in rice. Some WRKY family members (such as WRKY26) and some bHLH family members (such as late flowering) were selected as novel potential transcription factors involved in the regulation of Cu detoxification and Fe utilization, respectively. These genes were induced under corresponding stress conditions. Many Fe uptake-related genes were induced by Cu excess, while Cu detoxification-related genes were not induced by Fe deficiency. Meanwhile, some genes, such as metallothionein 3a, gibberellin 3beta-dioxygenase 2 and WRKY11, were induced by Cu excess but repressed by Fe deficiency. Concisely, our results highlight the crosstalk between Cu excess and Fe deficiency in rice. Cu excess caused Fe deficiency response, while Fe deficiency did not lead to Cu toxicity response. Metallothionein 3a might be responsible for Cu toxicity-induced chlorosis in rice. The crosstalk between Cu excess and Fe deficiency might be regulated by gibberellic acid.

Biofortification of Crops to Fight Anemia: Role of Vacuolar Iron Transporters

Plant-based foods provide all the crucial nutrients for human health. Among these, iron (Fe) is one of the essential micronutrients for plants and humans. A lack of Fe is a major limiting factor affecting crop quality, production, and human health. There are people who suffer from various health problems due to the low intake of Fe in their plant-based foods. Anemia has become a serious public health issue due to Fe deficiency. Enhancing Fe content in the edible part of food crops is a major thrust area for scientists worldwide. Recent progress in nutrient transporters has provided an opportunity to resolve Fe deficiency or nutritional problems in plants and humans. Understanding the structure, function, and regulation of Fe transporters is essential to address Fe deficiency in plants and to improve Fe content in staple food crops. In this review, we summarized the role of Fe transporter family members in the uptake, cellular and intercellular movement, and long-distance transport of Fe in plants. We draw insights into the role of vacuolar membrane transporters in the crop for Fe biofortification. We also provide structural and functional insights into cereal crops' vacuolar iron transporters (VITs). This review will help highlight the importance of VITs for improving the Fe biofortification of crops and alleviating Fe deficiency in humans.

S-Methylmethionine Effectively Alleviates Stress in Szarvasi-1 Energy Grass by Reducing Root-to-Shoot Cadmium Translocation

S-methylmethionine (SMM) is a universal metabolite of higher plants derived from L-methionine that has an approved priming effect under different types of abiotic and biotic stresses. Szarvasi-1 energy grass (Elymus elongatus subsp. ponticus cv. Szarvasi-1) is a biomass plant increasingly applied in phytoremediation to stabilize or extract heavy metals. In this study, Szarvasi-1 was grown in a nutrient solution. As a priming agent, SMM was applied in 0.02, 0.05 and 0.1 mM concentrations prior to 0.01 mM Cd addition. The growth and physiological parameters, as well as the accumulation pattern of Cd and essential mineral nutrients, were investigated. Cd exposure decreased the root and shoot growth, chlorophyll concentration, stomatal conductance, photosystem II function and increased the carotenoid content. Except for stomatal conductance, SMM priming had a positive effect on these parameters compared to Cd treatment without priming. In addition, it decreased the translocation and accumulation of Cd. Cd treatment decreased K, Mg, Mn, Zn and P in the roots, and K, S, Cu and Zn in the shoots compared to the untreated control. SMM priming changed the pattern of nutrient uptake, of which Fe showed characteristic accumulation in the roots in response to increasing SMM concentrations. We have concluded that SMM priming exerts a positive effect on Cd-stressed Szarvasi-1 plants, which retained their physiological performance and growth. This ameliorative effect is suggested to be based on, at least partly, the lower root-to-shoot Cd translocation by the upregulated Fe uptake and transport.

Fe fortification limits rice Cd accumulation by promoting root cell wall chelation and reducing the mobility of Cd in xylem

Fe biofortification and Cd mitigation in rice is essential for human health, thus the effects of fertilization with Fe on Cd uptake and distribution in rice need to be comprehensively studied. In this study, we investigated the roles of root iron (Fe)/manganese (Mn) plaques, root cell wall, organic acid, and expressions of Cd-transport related genes in restricting Cd uptake and translocation. The rice plants were exposed to 1 μM CdCl₂ with or without the addition of three doses of Fe at 5, 50, and 500 μM EDTA-Na₂Fe. The results showed that increasing supply of Fe remarkably reduced Cd accumulation in the shoots, mainly because of inhibited translocation of Cd from roots to shoots. As compared to 5 μM Fe treatment, 500 μM Fe significantly increased the ionic soluble pectin (ISP) content and decreased citric acid (CA) in the roots, thereby providing more Cd-binding sites in the cell wall of roots and reducing the mobility of Cd in xylem. Plant Fe status-mediated CA act as the main chelator for Cd mobilization, rather than through decreasing the pH. However, the plants supplied with low Fe or excess Fe facilitated the uptake of Cd in rice roots, as low Fe up-regulated the expression of Cd-transport related genes and excess Fe enhanced Cd enrichment on the root by iron plaque. Importantly, soil fertilization with Fe strongly reduced Cd accumulation in rice grain. Thus, optimizing the soil environmental Fe could effectively reduce Cd accumulation in the shoots by immobilizing Cd in the roots.

The basic leucine zipper transcription factor OsbZIP83 and the glutaredoxins OsGRX6 and OsGRX9 facilitate rice iron utilization under the control of OsHRZ ubiquitin ligases

Under low iron availability, plants induce the expression of various genes for iron uptake and translocation. The rice (Oryza sativa) ubiquitin ligases OsHRZ1 and OsHRZ2 cause overall repression of these iron-related genes at the transcript level, but their protein-level regulation is unclear. We conducted a proteome analysis to identify key regulators whose abundance was regulated by OsHRZs at the protein level. In response to iron deficiency or OsHRZ knockdown, many genes showed differential regulation between the transcript and protein levels, including the TGA-type basic leucine zipper transcription factor OsbZIP83. We also identified two glutaredoxins, OsGRX6 and OsGRX9, as OsHRZ-interacting proteins in yeast and plant cells. OsGRX6 also interacted with OsbZIP83. Our in vitro degradation assay suggested that OsbZIP83, OsGRX6 and OsGRX9 proteins are subjected to 26S proteasome- and OsHRZ-dependent degradation. Proteome analysis and our in vitro degradation assay also suggested that OsbZIP83 protein was preferentially degraded under iron-deficient conditions in rice roots. Transgenic rice lines overexpressing OsGRX9 and OsbZIP83 showed improved tolerance to iron deficiency. Expression of iron-related genes was affected in the OsGRX9 and OsGRX6 knockdown lines, suggesting disturbed iron utilization and signaling. OsbZIP83 overexpression lines showed enhanced expression of OsYSL2 and OsNAS3, which are involved in internal iron translocation, in addition to OsGRX9 and genes related to phytoalexin biosynthesis and the salicylic acid pathway. The results suggest that OsbZIP83, OsGRX6 and OsGRX9 facilitate iron utilization downstream of the OsHRZ pathway.

Field Studies on the Effect of Bioaugmentation with Bacillus amyloliquefaciens FZB42 on Plant Accumulation of Rare Earth Elements and Selected Trace Elements

This study is an investigation of the effect of soil bioaugmentation (inoculation) on a field scale with the commercially available product RhizoVital®42, containing Bacillus amyloliquefaciens FZB4, on element bioavailability, plant biomass production, as well as accumulation of rare earth elements (REEs), germanium, and selected trace elements. Zea mays and Helianthus annuus were selected as test plants. Post-harvest, results showed inoculation increased biomass production of Z. mays and H. annuus by 24% and 26%, albeit insignificant at p ≤ 0.05. Bioaugmentation enhanced Z. mays shoot content of P, Cd, and Ge by percentages between 73% and 80% (significant only for Ge) and decreased shoot content of REET, Pb, and Cu by 28%, 35%, and 59%, respectively. For H. annuus grown on bioaugmented soil, shoot content of Ca, Cu, Ge, REET, and Pb increased by over 40%, with a negligible decrease observed for Cd. Summarily, results suggest that bioaugmentation with Bacillus amyloliquefaciens FZB42 could enhance biomass production, increase soil element bioavailability enhance, and increase or reduce plant accumulation of target elements. Additionally, differences in P use efficiency could influence bioaugmentation effects on P accumulation.

Cadmium uptake and transport processes in rice revealed by stable isotope fractionation and Cd-related gene expression

Multiple processes are involved in Cd transfer in rice plants, including root uptake, xylem loading, and immobilization. These processes can be mediated by membrane transporters and can alter Cd speciation by binding Cd to different organic ligands. However, it remains unclear which processes control Cd transport in rice in response to different watering conditions in soil. Herein, Cd isotope fractionation and Cd-related gene expression were employed to investigate the key regulatory mechanisms during uptake, root-to-shoot, and stem-to-leaf transport of Cd in rice grown in pot experiments with Cd-contaminated soil under flooded and non-flooded conditions, respectively. The results showed that soil flooding decreased the Cd concentration in soil porewater and, thereby, Cd uptake and transport in rice. Cd isotopes fractionated negatively from soil porewater to the whole rice (flooded: ∆^114/110Cd_{rice-porewater} = -0.15‰, non-flooded: ∆^114/110Cd_{rice-porewater} = -0.39‰), suggesting that Cd transporters preferentially absorbed light Cd isotopes. The non-flooded treatment revealed an upregulated expression of OsNRAMP1 and OsNRAMP5 genes compared to the flooded treatment, which may partially contribute to its more pronounced porewater-to-rice fractionation. Cd isotopes fractionated positively from roots to shoots under flooded conditions (∆^114/110Cd_shoot-root = 0.19‰). However, a reverse direction of fractionation was observed under non-flooded conditions (∆^114/110Cd_shoot-root = -0.67‰), which was associated with the substantial upregulation of CAL1 in roots, facilitating xylem loading of Cd-CAL1 complexes with lighter isotopes. After being transported to the shoots, the majority of Cd were detained in stems (44%-55%), which were strongly enriched in lighter isotopes than in the leaves (∆^114/110Cd_leaf-stem = 0.77 to 1.01‰). Besides the Cd-CAL1 transported from the roots, the expression of OsPCS1 and OsHMA3 in the stems could also favor the enrichment of Cd-PCs with lighter isotopes, leaving heavier isotopes to be transported to the leaves. The higher expression levels of OsMT1e in older leaves than in younger leaves implied that Cd immobilization via binding to metallothioneins like OsMT1e may favor the enrichment of lighter isotopes in older leaves. The non-flooded treatment showed lighter Cd isotopes in younger leaves than the flooded treatment, suggesting that more Cd-CAL1 in the stems and Cd-PCs in the older leaves might be transported to the younger leaves under non-flooded conditions. Our results demonstrate that isotopically light Cd can be preferentially transported from roots to shoots when more Cd is absorbed by rice under non-flooded conditions, and isotope fractionation signature together with gene expression quantification has the potential to provide a better understanding of the key processes regulating Cd transfer in rice.

Mapping of the Quantitative Trait Loci and Candidate Genes Associated With Iron Efficiency in Maize

Iron (Fe) is a mineral micronutrient for plants, and Fe deficiency is a major abiotic stress in crop production because of its low solubility under aerobic and alkaline conditions. In this study, 18 maize inbred lines were used to preliminarily illustrate the physiological mechanism underlying Fe deficiency tolerance. Then biparental linkage analysis was performed to identify the quantitative trait loci (QTLs) and candidate genes associated with Fe deficiency tolerance using the recombinant inbred line (RIL) population derived from the most Fe-efficient (Ye478) and Fe-inefficient (Wu312) inbred lines. A total of 24 QTLs was identified under different Fe nutritional status in the Ye478 × Wu312 RIL population, explaining 6.1-26.6% of phenotypic variation, and ten candidate genes were identified. Plants have evolved two distinct mechanisms to solubilize and transport Fe to acclimate to Fe deficiency, including reduction-based strategy (strategy I) and chelation-based strategy (strategy II), and maize uses strategy II. However, not only genes involved in Fe homeostasis verified in strategy II plants (strategy II genes), which included ZmYS1, ZmYS3, and ZmTOM2, but also several genes associated with Fe homeostasis in strategy I plants (strategy I genes) were identified, including ZmFIT, ZmPYE, ZmILR3, ZmBTS, and ZmEIN2. Furthermore, strategy II gene ZmYS1 and strategy I gene ZmBTS were significantly upregulated in the Fe-deficient roots and shoots of maize inbred lines, and responded to Fe deficiency more in shoots than in roots. Under Fe deficiency, greater upregulations of ZmYS1 and ZmBTS were observed in Fe-efficient parent Ye478, not in Fe-inefficient parent Wu312. Beyond that, ZmEIN2 and ZmILR3, were found to be Fe deficiency-inducible in the shoots. These findings indicate that these candidate genes may be associated with Fe deficiency tolerance in maize. This study demonstrates the use of natural variation to identify important Fe deficiency-regulated genes and provides further insights for understanding the response to Fe deficiency stress in maize.

A transcriptomic view of cadmium retention in roots of cadmium-safe rice line (Oryza sativa L.)

A better understanding of the mechanisms controlling cadmium (Cd) accumulation in rice will benefit the development of strategies to minimize Cd accumulation in grains. A Cd-safe rice line designated D62B accumulated less than 0.2 mg Cd kg^-1 in brown rice due to its strong capacity for Cd retention in roots. Here transcriptomic was used to clarify the underlying mechanisms of Cd response in roots of D62B compared with a high Cd-accumulating line (Wujin4B). There were 777, 1058 differentially expressed genes (DEGs) in D62B and Wujin4B, respectively, when exposed to Cd. The functions of DEGs were clearly line-specific. Cell wall biosynthesis responded more intensively to Cd stress in D62B, facilitating Cd restriction. Meanwhile, more glutathione (GSH) and phytochelatins synthesized in D62B with the upregulation of sulphur and GSH metabolism. Besides, membrane proteins played critical roles in Cd response in D62B, whereas 18 terms involved in regulation were enriched in Wujin4B. Exogenous GSH further induced the expression of genes related to GSH metabolism and cell wall biosynthesis, leading to the retention of more Cd. Great responsiveness of cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of Cd-safe rice line.

Vacuolar Iron Transporter (Like) proteins: Regulators of cellular iron accumulation in plants

Iron is not only important for plant physiology, but also a very important micronutrient in human diets. The vacuole is the main site for accumulation of excess amounts of various nutrients and toxic substances in plant cells. During the past decade, many Vacuolar Iron Transporter (VIT) and VIT-Like (VTL) genes have been identified and shown to play important roles in iron homeostasis in different plants. Furthermore, recent reports identified novel roles of these transporter genes in symbiotic nitrogen fixation (SNF) in legume crops as well as in the blue coloration of petals in flowers. The literature indicates their universal role in Fe transport across different tissues (grains, nodules, flowers) to different biological processes (cellular iron homeostasis, SNF, petal coloration) in different plants. Here, we have systematically reviewed different aspects, such as structure, molecular evolution, expression, and function of VIT/VTL proteins. This will help future studies aimed at functional analysis of VIT/VTL genes in other plant species, vacuolar transportation mechanisms, and iron biofortification at large.

Iron deficiency-inducible peptide-coding genes OsIMA1 and OsIMA2 positively regulate a major pathway of iron uptake and translocation in rice

Under low iron (Fe) availability, plants transcriptionally induce various genes responsible for Fe uptake and translocation to obtain adequate amounts of Fe. Although transcription factors and ubiquitin ligases involved in these Fe deficiency responses have been identified, the mechanisms coordinating these pathways have not been clarified in rice. Recently identified Fe-deficiency-inducible IRON MAN (IMA)/FE UPTAKE-INDUCING PEPTIDE (FEP) positively regulates many Fe-deficiency-inducible genes for Fe uptake in Arabidopsis. Here, we report that the expression of two IMA/FEP genes in rice, OsIMA1 and OsIMA2, is strongly induced under Fe deficiency, positively regulated by the transcription factors IDEF1, OsbHLH058, and OsbHLH059, as well as OsIMA1 and OsIMA2 themselves, and negatively regulated by HRZ ubiquitin ligases. Overexpression of OsIMA1 or OsIMA2 in rice conferred tolerance to Fe deficiency and accumulation of Fe in leaves and seeds. These OsIMA-overexpressing rice exhibited enhanced expression of all of the known Fe-deficiency-inducible genes involved in Fe uptake and translocation, except for OsYSL2, a Fe-nicotianamine transporter gene, in roots but not in leaves. Knockdown of OsIMA1 or OsIMA2 caused minor effects, including repression of some Fe uptake- and translocation-related genes in OsIMA1 knockdown roots. These results indicate that OsIMA1 and OsIMA2 play key roles in enhancing the major pathway of the Fe deficiency response in rice.

γ-Aminobutyric Acid Suppresses Iron Transportation from Roots to Shoots in Rice Seedlings by Inducing Aerenchyma Formation

γ-Aminobutyric acid (GABA) is a widely distributed non-protein amino acid mediated the regulation of nitrate uptake and Al³⁺ tolerance in plants. However, there are few reports about the involvement of GABA in the regulation of iron (Fe) acquisition and translocation. Here, we show that GABA regulates Fe homeostasis in rice seedlings. Exogenous GABA decreased the chlorophyll concentration in leaves, with or without Fe supply. Over-expression of glutamate decarboxylase (GAD) gene, coding a crucial enzyme of GABA production, elevated endogenous GABA content and caused more leaf chlorosis than wild type (Nipponbare). GABA inhibited Fe transportation from roots to shoots and GABA application elevated the expression levels of Fe deficiency (FD)-related genes under conditions of Fe-sufficiency (FS), suggesting that GABA is a regulator of Fe translocation. Using Perls’ blue staining, we found that more ferric iron (Fe³⁺) was deposited in the epidermal cells of roots treated with GABA compared with control roots. Anatomic section analysis showed that GABA treatment induced more aerenchyma formation compared with the control. Aerenchyma facilitated the oxidization of soluble ferrous iron (Fe²⁺) into insoluble Fe³⁺, resulted in Fe precipitation in the epidermis, and inhibited the transportation of Fe from roots to shoots.

Cadmium toxicity reduction in rice (Oryza sativa L.) through iron addition during primary reaction of photosynthesis

Cadmium (Cd) pollution is a worldwide concern due to its biotoxicity. Because Cd and Fe are closely associated during plant photosynthesis, this study aims at investigating the mechanism governing Cd toxicity during photosynthetic primary reaction in rice by adjusting Fe concentration. The results show that moderate Fe concentration (1.0 g kg^-1) added to soil can increase the stomatal conductance (Gs) and SPAD value by stimulating the stomatal opening and chlorophyll synthesis. Moderate Fe concentration can also improve the maximum fluorescence (Fm) and the maximal photochemical efficiency (Fv/Fm) to keep the high reaction center activity and electronic transfer efficiency in photosystems I and II. Thus, moderate Fe can eliminate Cd-induced decrease in Gs, intercellular CO₂ concentration (Ci) and net photosynthetic rate (Pn) as well as the disorder of antioxidative system under Cd concentration of 2.0 mg kg^-1 in the soil. When its application is increased to 2.0 g kg^-1, Fe can notably decrease Pn, and result in remarkable decrease in the biomass of shoots and grains. Decrease in Pn can be mainly attributed to high Fe concentration which can greatly destroy chloroplast structure and, meanwhile, inhibit the electron transfer between acceptor and donator in photosynthetic chain especially from quinone A (Q_A) to quinone B (Q_B). Unlike the situation under moderate Fe concentration, the high Fe application cannot mitigate the Cd-induced decrease in photosynthetic index. Our results indicate that the moderate Fe application is necessary to promote rice performance and production and, in the meantime, to inhibit Cd toxicity in the extensively polluted soils.

Chelators of iron and their role in plant's iron management

Proper transport of metal and their homeostasis is very crucial for the growth and development of plants. Plants root are the primary organs which comes in contact with the stress and thus few modifications occurs, often determining the nutrient efficiency or sometimes as a stress tolerance mechanism. Plant utilizes two strategies for the uptake of iron viz, strategy I-reduction based and strategy II-chelation based. In this review we attempted for a better understanding of how the chelators acts in the mechanism of iron uptake from soils to plants and how iron is distributed in the plants.

Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification

Iron (Fe) and sulfur (S) are two essential elements for plants, whose interrelation is indispensable for numerous physiological processes. In particular, Fe homeostasis in cereal species is profoundly connected to S nutrition because phytosiderophores, which are the metal chelators required for Fe uptake and translocation in cereals, are derived from a S-containing amino acid, methionine. To date, various biotechnological cereal Fe biofortification strategies involving modulation of genes underlying Fe homeostasis have been reported. Meanwhile, the resultant Fe-biofortified crops have been minimally characterized from the perspective of interaction between Fe and S, in spite of the significance of the crosstalk between the two elements in cereals. Here, we intend to highlight the relevance of Fe and S interrelation in cereal Fe homeostasis and illustrate the potential implications it has to offer for future cereal Fe biofortification studies.

Silicon reduces the iron uptake in rice and induces iron homeostasis related genes

Gramineous plants take up silicon (Si) that enhances the formation of exodermal Casparian bands (CBs) in the roots of rice (Oryza sativa L.). Furthermore, it is known that Si supply reduces the concentration of Fe in rice shoots. We hypothesized that the Si-enhanced CB formation in the exodermis reduces in the flux of Fe in the apoplast and the uptake of Fe loaded deoxymugineic acid. Thus, the effect of silicic acid supply at varied Fe concentrations and Fe forms was investigated in nutrient solution. The Fe concentrations in the shoot and apoplastic Fe concentrations in the root were determined and an Affymetrix GeneChip experiment was carried out together with qRT-PCR measurements for observation of transcriptomic reactions. Additionally, the Fe uptake of an overexpression mutant of OsABCG25 with an enhanced exodermal CB formation was investigated. The application of silicic acid reduced the Fe concentrations in shoot DM independently of the supplied Fe concentration and Fe form. As a reaction to the Fe shortage, the full cascade of Fe-homeostasis-related genes in the roots was upregulated. Silicic acid supply also decreased the apoplastic Fe concentrations in roots. In addition, an overexpression mutant of OsABCG25 with an enhanced CB formation showed a reduced uptake of Fe in excess Fe conditions. The results suggest that the Si-induced CB formation in the exodermis hampers the flux of Fe into the apoplast of the cortex and, thus, Fe uptake of rice grown in nutrient solution which is reflected in the upregulation of Fe homeostasis-related genes.

Cadmium absorption and translocation of amaranth (Amaranthus mangostanus L.) affected by iron deficiency

Amaranth (Amaranthus mangostanus L.) has superior capability for accumulating cadmium (Cd) and has the potential to be used for phytoremediation of Cd contaminated soils. Iron (Fe) is chemically similar to Cd and may mediate Cd-induced physiological or metabolic impacts in plants. The purpose was to investigate the model of time-dependent and concentration-dependent kinetics of Cd absorption under Fe deficiency, understanding the physiological mechanism of Cd absorption in amaranth roots. The kinetic characteristics of Cd uptake by amaranth grown in Cd enriched nutritional solution with or without Fe addition and with methanol-chloroform, carbonyl cyanide 3-chlorophenylhydrazone (CCCP), and lanthanum chloride (LaCl₃) were compared using ¹⁰⁹Cd²⁺ isotope labeling technique. The results showed that Cd uptake was time-dependent and about 90-93% of uptake occurred during the first 150 min. The kinetics of Cd uptake showed that two stages were involved. The saturation stage fitted the Michaelis-Menten model when concentrations of Cd were lower than 12.71 μmol/L and then the absorption of Cd by roots was increased linearly during the second stage. Only linear absorption was observed with methanol-chloroform treatment while the metabolic inhibitor CCCP inhibited only the saturation absorption process, and the Ca channel inhibitor LaCl₃ partially inhibited the two stages of absorption. These results indicated that the root absorption of ¹⁰⁹Cd²⁺ was enhanced under Fe deficiency which induced more Fe transporters in the root cell membrane, and the Ca channel, apoplastic and symplastic pathways enhanced the Cd absorption in roots.

The Molecular Mechanisms Underlying Iron Deficiency Responses in Rice

Iron (Fe) is an essential element required for plant growth and development. Under Fe-deficientconditions, plants have developed two distinct strategies (designated as strategy I and II) to acquire Fe from soil. As a graminaceous species, rice is not a typical strategy II plant, as it not only synthesizes DMA (2'-deoxymugineic acid) in roots to chelate Fe3+ but also acquires Fe2+ through transporters OsIRT1 and OsIRT2. During the synthesis of DMA in rice, there are three sequential enzymatic reactions catalyzed by enzymes NAS (nicotianamine synthase), NAAT (nicotianamine aminotransferase), and DMAS (deoxymugineic acid synthase). Many transporters required for Fe uptake from the rhizosphere and internal translocation have also been identified in rice. In addition, the signaling networks composed of various transcription factors (such as IDEF1, IDEF2, and members of the bHLH (basic helix-loop-helix) family), phytohormones, and signaling molecules are demonstrated to regulate Fe uptake and translocation. This knowledge greatly contributes to our understanding of the molecular mechanisms underlying iron deficiency responses in rice.

OsbHLH058 and OsbHLH059 transcription factors positively regulate iron deficiency responses in rice

Subgroup IVc basic helix-loop-helix transcription factors OsbHLH058 and OsbHLH059 positively regulate major iron deficiency responses in rice in a similar but distinct manner, putatively under partial control by OsHRZs. Under low iron availability, plants transcriptionally induce the expression of genes involved in iron uptake and translocation. OsHRZ1 and OsHRZ2 ubiquitin ligases negatively regulate this iron deficiency response in rice. The basic helix-loop-helix (bHLH) transcription factor OsbHLH060 interacts with OsHRZ1, and positively regulates iron deficiency-inducible genes. However, the functions of three other subgroup IVc bHLH transcription factors in rice, OsbHLH057, OsbHLH058, and OsbHLH059, have not yet been characterized. In the present study, we investigated the functions of OsbHLH058 and OsbHLH059 related to iron deficiency response. OsbHLH058 expression was repressed under iron deficiency, whereas the expression of OsbHLH057 and OsbHLH060 was moderately induced. Yeast two-hybrid analysis indicated that OsbHLH058 interacts with OsHRZ1 and OsHRZ2 more strongly than OsbHLH060, whereas OsbHLH059 showed no interaction. An in vitro ubiquitination assay detected no OsbHLH058 and OsbHLH060 ubiquitination by OsHRZ1 and OsHRZ2. Transgenic rice lines overexpressing OsbHLH058 showed tolerance for iron deficiency and higher iron concentration in seeds. These lines also showed enhanced expression of many iron deficiency-inducible genes involved in iron uptake and translocation under iron-sufficient conditions. Conversely, OsbHLH058 knockdown lines showed susceptibility to iron deficiency and reduced expression of many iron deficiency-inducible genes. OsbHLH059 knockdown lines were also susceptible to iron deficiency, and formed characteristic brownish regions in iron-deficient new leaves. OsbHLH059 knockdown lines also showed reduced expression of many iron deficiency-inducible genes. These results indicate that OsbHLH058 and OsbHLH059 positively regulate major iron deficiency responses in a similar but distinct manner, and that this function may be partially controlled by OsHRZs.

OsZIP1 functions as a metal efflux transporter limiting excess zinc, copper and cadmium accumulation in rice

BACKGROUND

Metal homeostasis is critical for plant growth, development and adaptation to environmental stresses and largely governed by a variety of metal transporters. The plant ZIP (Zn-regulated transporter, Iron-regulated transporter-like Protein) family proteins belong to the integral membrane transporters responsible for uptake and allocation of essential and non-essential metals. However, whether the ZIP family members mediate metal efflux and its regulatory mechanism remains unknown.

RESULTS

In this report, we provided evidence that OsZIP1 is a metal-detoxified transporter through preventing excess Zn, Cu and Cd accumulation in rice. OsZIP1 is abundantly expressed in roots throughout the life span and sufficiently induced by excess Zn, Cu and Cd but not by Mn and Fe at transcriptional and translational levels. Expression of OsZIP-GFP fusion in rice protoplasts and tobacco leaves shows that OsZIP1 resides in the endoplasmic reticulum (ER) and plasma membrane (PM). The yeast (Saccharomyces cerevisiae) complementation test shows that expression of OsZIP1 reduced Zn accumulation. Transgenic rice overexpressing OsZIP1 grew better under excess metal stress but accumulated less of the metals in plants. In contrast, both oszip1 mutant and RNA interference (RNAi) lines accumulated more metal in roots and contributed to metal sensitive phenotypes. These results suggest OsZIP1 is able to function as a metal exporter in rice when Zn, Cu and Cd are excess in environment. We further identified the DNA methylation of histone H3K9me2 of OsZIP1 and found that OsZIP1 locus, whose transcribed regions imbed a 242 bp sequence, is demethylated, suggesting that epigenetic modification is likely associated with OsZIP1 function under Cd stress.

CONCLUSION

OsZIP1 is a transporter that is required for detoxification of excess Zn, Cu and Cd in rice.

Characterization of the Cd-resistant fungus Aspergillus aculeatus and its potential for increasing the antioxidant activity and photosynthetic efficiency of rice

Considerable evidence exists that microorganisms play a significant role in the remediation of soil contaminated with heavy metals. Aspergillus aculeatus (A. aculeatus) isolated from Cd-polluted soil has been shown to increase the tolerance of turfgrasses to Cd stress. In this study, we assessed the tolerance, biosorption capacity for Cd and surface characteristics of this fungus and investigated the effect of plant inoculation with A. aculeatus on the lipid peroxidation, antioxidant activities and photosynthetic rates in rice cultivated in Cd-contaminated soil. The results indicated that the removal efficiency of A. aculeatus was 46.8% at a Cd concentration of 10 mg L^-1. The A. aculeatus strains had the capacity to produce indole acetic acid, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase and to solubilize phosphate. The O₂^- accumulation and the amount of MDA in rice roots inoculated with A. aculeatus were significantly lower than those in uninoculated plants. Nevertheless, no decrease in leaf ROS accumulation and photosynthetic activity was observed between the inoculated and uninoculated plants. Inoculation with A. aculeatus contained more of the ROS-scavenging metabolite GSH, a higher GSH/GSSG ratio, and higher antioxidative enzyme (SOD, POD, and CAT) activities, possibly explaining the lower ROS concentrations observed in inoculated roots in the presence of Cd. These results suggest that application of A. aculeatus has the potential to protect crops against Cd stress.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

Iron transport and its regulation in plants

Iron is an essential element for plants as well as other organisms, functioning in various cellular processes, including respiration, chlorophyll biosynthesis, and photosynthesis. Plants take up iron from soil in which iron solubility is extremely low especially under aerobic conditions at high-pH range. Therefore, plants have evolved efficient iron-uptake mechanisms. Because iron is prone to being precipitated and excess ionic iron is cytotoxic, plants also have sophisticated internal iron-transport mechanisms. These transport mechanisms comprise iron chelators including nicotianamine, mugineic acid family phytosiderophores and citrate, and various types of transporters of these chelators, iron-chelate complexes, or free iron ions. To maintain iron homeostasis, plants have developed mechanisms for regulating gene expression in response to iron availability. Expression of various genes involved in iron uptake and translocation is induced under iron deficiency by transcription factor networks and is negatively regulated by the ubiquitin ligase HRZ/BTS. This response is deduced to be mediated by cellular iron sensing as well as long-distance iron signaling. The ubiquitin ligase HRZ/BTS is a candidate intracellular iron sensor because it binds to iron and zinc, and its activity is affected by iron availability. The iron-excess response of plants is thought to be partially independent of the iron-deficiency response. In this review, we summarize and discuss extant knowledge of plant iron transport and its regulation.

Site-specific regulation of transcriptional responses to cadmium stress in the hyperaccumulator, Sedum alfredii: based on stem parenchymal and vascular cells

We compared the transcriptomes of parenchymal and vascular cells of Sedum alfredii stem under Cd stress to reveal gene regulatory networks underlying Cd hyperaccumulation. Cadmium (Cd) hyperaccumulation in plants is a complex biological process controlled by gene regulatory networks. Efficient transport through vascular systems and storage by parenchymal cells are vital for Cd hyperaccumulation in the Cd hyperaccumulator Sedum alfredii, but the genes involved are poorly understood. We investigated the spatial gene expression profiles of transport and storage sites in S. alfredii stem using laser-capture microdissection coupled with RNA sequencing. Gene expression patterns in response to Cd were distinct in vascular and parenchymal cells, indicating functional divisions that corresponded to Cd transportation and storage, respectively. In vascular cells, plasma membrane-related terms enriched a large number of differentially-expressed genes (DEGs) for foundational roles in Cd transportation. Parenchymal cells contained considerable DEGs specifically concentrated on vacuole-related terms associated with Cd sequestration and detoxification. In both cell types, DEGs were classified into different metabolic pathways in a similar way, indicating the role of Cd in activating a systemic stress signalling network where ATP-binding cassette transporters and Ca²⁺ signal pathways were probably involved. This study identified site-specific regulation of transcriptional responses to Cd stress in S. alfredii and analysed a collection of genes that possibly function in Cd transportation and detoxification, thus providing systemic information and direction for further investigation of Cd hyperaccumulation molecular mechanisms.

Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice

Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.

Characterization of the Nicotianamine Exporter ENA1 in Rice

Under iron (Fe) deficiency, graminaceous plants produce and secrete Fe-chelating phytosiderophores of the mugineic acid (MA) family into the rhizosphere to solubilize and mediate uptake of sparingly soluble Fe in the soil. MAs and their biosynthetic intermediate, nicotianamine (NA), are also important for the translocation of divalent metals such as Fe and zinc (Zn) throughout the plant body. In this study, the physiological role of the efflux transporter EFFLUX TRANSPORTER OF NA (ENA1), which exports NA out of cells, was analyzed in rice. Promoter-GUS analysis showed that ENA1 was mainly expressed in roots, and strongly upregulated under Fe-deficient conditions. In epidermal onion cells and rice roots, green fluorescent protein-tagged ENA1 localized mainly to the plasma membrane, while a part of the fluorescence was observed in vesicular structures in the cytoplasm. In the younger stage after germination, ENA1-overexpressing rice plants exhibited truncated roots with many root hairs compared to wild-type plants, while these phenotype were not observed in high Zn-containing medium. In Arabidopsis, which use a different strategy for Fe uptake from rice, ENA1 overexpression did not show any apparent phenotypes. Oligo DNA microarray analysis in rice showed that ENA1 knockout affects the response to stress, especially in root plastids. These results suggest that ENA1 might be recycling between the plasma membrane and cellular compartments by vesicular transport, playing an important role in the transport of NA, which is important for the physiological response to Fe deficiency.

Association Study Reveals Genetic Loci Responsible for Arsenic, Cadmium and Lead Accumulation in Rice Grain in Contaminated Farmlands

Accumulation of toxic heavy metals and metalloids (THMMs) in crop grain remarkably affects food safety and human health. Reducing the content of THMMs in grain requires the identification and manipulation of the genes regulating their accumulation. This study aimed to determine the genetic variations affecting grain THMM accumulation in rice by using association mapping. We used 276 accessions with 416 K single nucleotide polymorphisms (SNPs) and performed genome-wide association analysis of grain THMM concentrations in rice grown in heavily multi-contaminated farmlands. We detected 22, 17, and 21 quantitative trait loci (QTLs) for grain arsenic, cadmium, and lead concentrations, respectively. Both inter- and intra-subpopulation variants accounted for these QTLs. Most QTLs contained no known THMM-related genes and represented unidentified novel genes. We examined the candidate genes in qGAS1, a QTL for grain arsenic concentration with the best P-value detected for the entire population. We speculated that a transport protein of the multidrug and toxin extrusion family could be the candidate gene for this QTL. Our study suggested that the genetic regulation of grain THMM accumulation is very complex and largely unknown. The QTLs and SNPs identified in this study might help in the identification of new genes regulating THMM accumulation and aid in marker-assisted breeding of rice with low grain THMM content.

Molecular processes in iron and zinc homeostasis and their modulation for biofortification in rice

More than a billion people suffer from iron or zinc deficiencies globally. Rice (Oryza sativa L.) iron and zinc biofortification; i.e., intrinsic iron and zinc enrichment of rice grains, is considered the most effective way to tackle these deficiencies. However, rice iron biofortification, by means of conventional breeding, proves difficult due to lack of sufficient genetic variation. Meanwhile, genetic engineering has led to a significant increase in the iron concentration along with zinc concentration in rice grains. The design of impactful genetic engineering biofortification strategies relies upon vast scientific knowledge of precise functions of different genes involved in iron and zinc uptake, translocation and storage. In this review, we present an overview of molecular processes controlling iron and zinc homeostasis in rice. Further, the genetic engineering approaches adopted so far to increase the iron and zinc concentrations in polished rice grains are discussed in detail, highlighting the limitations and/or success of individual strategies. Recent insight suggests that a few genetic engineering strategies are commonly utilized for elevating iron and zinc concentrations in different genetic backgrounds, and thus, it is of great importance to accumulate scientific evidence for diverse genetic engineering strategies to expand the pool of options for biofortifying farmer-preferred cultivars.

Engineering rice with lower grain arsenic

Arsenic (As) is a poisonous element that causes severe skin lesions and cancer in humans. Rice (Oryza sativa L.) is a major dietary source of As in humans who consume this cereal as a staple food. We hypothesized that increasing As vacuolar sequestration would inhibit its translocation into the grain and reduce the amount of As entering the food chain. We developed transgenic rice plants expressing two different vacuolar As sequestration genes, ScYCF1 and OsABCC1, under the control of the RCc3 promoter in the root cortical and internode phloem cells, along with a bacterial γ-glutamylcysteine synthetase driven by the maize UBI promoter. The transgenic rice plants exhibited reduced root-to-shoot and internode-to-grain As translocation, resulting in a 70% reduction in As accumulation in the brown rice without jeopardizing agronomic traits. This technology could be used to reduce As intake, particularly in populations of South East Asia suffering from As toxicity and thereby improve human health.

Annotation and characterization of Cd-responsive metal transporter genes in rapeseed (Brassica napus)

In higher plants, heavy metal transporters are responsible for metal uptake, translocation and homeostasis. These metals include essential metals such as zinc (Zn) or manganese (Mn) and non-essential metals like cadmium (Cd) or lead (Pb). Although a few heavy metal transporters have been well identified in model plants (e.g. Arabidopsis and rice), little is known about their functionality in rapeseed (Brassica napus). B. napus is an important oil crop ranking the third largest sources of vegetable oil over the world. Importantly, B. napus has long been considered as a desirable candidate for phytoremediation owning to its massive dry weight productivity and moderate to high Cd accumulation. In this study, 270 metal transporter genes (MTGs) from B. napus genome were identified and annotated using bioinformatics and high-throughput sequencing. Most of the MTGs (74.8%, 202/270) were validated by RNA-sequencing (RNA-seq) the seedling libraries. Based on the sequence identity, nine superfamilies including YSL, OPT, NRAMP, COPT, ZIP, CDF/MTP, HMA, MRP and PDR have been classified. RNA-sequencing profiled 202 non-redundant MTGs from B. napus seedlings, of which, 108 MTGs were differentially expressed and 62 genes were significantly induced under Cd stress. These differentially expressed genes (DEGs) are dispersed in the rapeseed genome. Some of the genes were well confirmed by qRT-PCR. Analysis of the genomic distribution of MTGs on B. napus chromosomes revealed that their evolutional expansion was probably through localized allele duplications.

Influence and interaction of iron and cadmium on photosynthesis and antioxidative enzymes in two rice cultivars

In this study, a soil pot experiment was conducted to investigate the changes in photosynthesis and antioxidative enzymes in two rice varieties (Shendao 6 and Shennong 265) supplied with iron (Fe), cadmium (Cd), and Fe and Cd together. The concentrations of Fe and Cd in the soil were 0, 1.0 g Fe·kg^-1 and 0, 2.0 mg Cd·kg^-1, respectively. Photosynthetic indices and antioxidative enzyme activities were recorded at different rice growth stages. At the early stage, Cd showed a transient stimulatory effect on the photosynthetic rate of Shennong 265. For Shendao 6, however, Cd showed a transient stimulatory effect on photosynthetic rate, intercellular CO₂ concentration, stomatal conductance and transpiration efficiency. In addition, the results show that Cd can also enhance the superoxide dismutase (SOD) and peroxidase (POD) activities, but reduce the malondialdehyde (MDA) and soluble protein contents in the two rice cultivars. Subsequently, Cd starts to inhibit photosynthesis and SOD activity until the ripening stage, causing the lowest photosynthetic rate and SOD activity at this stage. In contrast, Fe alleviates the Cd-induced changes at earlier or later growth stage. Notably at the later growth stage, the results show that the interaction between Fe and Cd increases the SOD and catalase (CAT) activities, while decreasing the lipid peroxidation and promoting photosynthesis. As a result, it ultimately increases the biomass. The results from this study suggest that Fe (as Fe fertilizer) is a promising alternative for agricultural use to enhance the plant development and, simultaneously, to reduce Cd toxicity in extensively polluted soils.

Transcriptome Analysis Reveals the Response of Iron Homeostasis to Early Feeding by Small Brown Planthopper in Rice

It has been documented that planthopper attacks change iron (Fe) content of rice plants. To investigate whether planthopper attacks change rice Fe homeostasis at the molecular level, the response of rice Fe homeostasis to early feeding by small brown planthopper (SBPH) was examined by transcriptome profiling. Results showed that the concentration of Fe and nicotianamine decreased in resistant rice genotype and increased in susceptible rice genotype after attack by SBPH. Transcriptome profiling showed that 13 and 21 Fe homeostasis-related genes encoded enzymes that were involved in phytosiderophore biosynthesis and that Fe transporters and regulators displayed altered expression in resistant and susceptible rice genotypes, respectively, after attack by SBPH. This revealing response of Fe homeostasis to planthopper attack in rice at the molecular level provided new insight into rice plants' response to planthopper attack and uncovered a novel physiological response of rice to planthopper attack, which extended our knowledge of the early interaction between rice and SBPH.

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant.

Comparison on cellular mechanisms of iron and cadmium accumulation in rice: prospects for cultivating Fe-rich but Cd-free rice

Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice. This comprehensive review systematically elaborates and compares cellular mechanisms of Fe/Cd uptake and accumulation in rice, respectively. Mechanisms for maintaining Fe homeostasis and Cd detoxicification are also elucidated. Then, effects of different fertilizer management on Fe/Cd accumulation in rice are discussed. Finally, this review enumerates various approaches for reducing grain Cd accumulation and enhancing Fe content in rice. In summary, understanding of discrepant cellular mechanisms of Fe/Cd accumulation in rice provides guidance for cultivating Fe-fortified rice and has paved the way to develop rice that are tolerant to Cd stress, aiming at breeding Fe-rich but Cd-free rice.

Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation

Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices.

Characterization of long non-coding RNAs involved in cadmium toxic response in Brassica napus

There is increasing evidence of long non-coding RNA (lncRNA) involvement in a variety of biological responses to environmental stresses.

The Phytosiderophore Efflux Transporter TOM2 Is Involved in Metal Transport in Rice

Iron is an essential metal element for all living organisms. Graminaceous plants produce and secrete mugineic acid family phytosiderophores from their roots to acquire iron in the soil. Phytosiderophores chelate and solubilize insoluble iron hydroxide in the soil. Subsequently, plants take up iron-phytosiderophore complexes through specific transporters on the root cell membrane. Phytosiderophores are also thought to be important for the internal transport of various transition metals, including iron. In this study, we analyzed TOM2 and TOM3, rice homologs of transporter of mugineic acid family phytosiderophores 1 (TOM1), a crucial efflux transporter directly involved in phytosiderophore secretion into the soil. Transgenic rice analysis using promoter-β-glucuronidase revealed that TOM2 was expressed in tissues involved in metal translocation, whereas TOM3 was expressed only in restricted parts of the plant. Strong TOM2 expression was observed in developing tissues during seed maturation and germination, whereas TOM3 expression was weak during seed maturation. Transgenic rice in which TOM2 expression was repressed by RNA interference showed growth defects compared with non-transformants and TOM3-repressed rice. Xenopus laevis oocytes expressing TOM2 released (14)C-labeled deoxymugineic acid, the initial phytosiderophore compound in the biosynthetic pathway in rice. In onion epidermal and rice root cells, the TOM2-GFP fusion protein localized to the cell membrane, indicating that the TOM2 protein is a transporter for phytosiderophore efflux to the cell exterior. Our results indicate that TOM2 is involved in the internal transport of deoxymugineic acid, which is required for normal plant growth.

Laser capture microdissection in Ectocarpus siliculosus: the pathway to cell-specific transcriptomics in brown algae

Laser capture microdissection (LCM) facilitates the isolation of individual cells from tissue sections, and when combined with RNA amplification techniques, it is an extremely powerful tool for examining genome-wide expression profiles in specific cell-types. LCM has been widely used to address various biological questions in both animal and plant systems, however, no attempt has been made so far to transfer LCM technology to macroalgae. Macroalgae are a collection of widespread eukaryotes living in fresh and marine water. In line with the collective effort to promote molecular investigations of macroalgal biology, here we demonstrate the feasibility of using LCM and cell-specific transcriptomics to study development of the brown alga Ectocarpus siliculosus. We describe a workflow comprising cultivation and fixation of algae on glass slides, laser microdissection, and RNA amplification. To illustrate the effectiveness of the procedure, we show qPCR data and metrics obtained from cell-specific transcriptomes generated from both upright and prostrate filaments of Ectocarpus.

Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Plants are exposed to a wide range of abiotic stresses (AS), which often occur in combination. Because physiological investigations typically focus on one stress, our understanding of unspecific stress responses remains limited. The plant redox homeostasis, i.e., the production and removal of reactive oxygen species (ROS), may be involved in many environmental stress conditions. Therefore, this study intended to identify genes, which are activated in diverse AS, focusing on ROS-related pathways. We conducted a meta-analysis (MA) of microarray experiments, focusing on rice. Transcriptome data were mined from public databases and fellow researchers, which represented 36 different experiments and investigated diverse AS, including ozone stress, drought, heat, cold, salinity, and mineral deficiencies/toxicities. To overcome the inherent artifacts of different MA methods, data were processed using Fisher, rOP, REM, and product of rank (GeneSelector), and genes identified by most approaches were considered as shared differentially expressed genes (DEGs). Two MA strategies were adopted: first, datasets were separated into shoot, root, and seedling experiments, and these tissues were analyzed separately to identify shared DEGs. Second, shoot and seedling experiments were classed into oxidative stress (OS), i.e., ozone and hydrogen peroxide treatments directly producing ROS in plant tissue, and other AS, in which ROS production is indirect. In all tissues and stress conditions, genes a priori considered as ROS-related were overrepresented among the DEGs, as they represented 4% of all expressed genes but 7-10% of the DEGs. The combined MA approach was substantially more conservative than individual MA methods and identified 1001 shared DEGs in shoots, 837 shared DEGs in root, and 1172 shared DEGs in seedlings. Within the OS and AS groups, 990 and 1727 shared DEGs were identified, respectively. In total, 311 genes were shared between OS and AS, including many regulatory genes. Combined co-expression analysis identified among those a cluster of 42 genes, many involved in the photosynthetic apparatus and responsive to drought, iron deficiency, arsenic toxicity, and ozone. Our data demonstrate the importance of redox homeostasis in plant stress responses and the power of MA to identify candidate genes underlying unspecific signaling pathways.

Iron deficiency responses in rice roots

Iron (Fe) is an essential element for most living organisms. To acquire sparingly soluble Fe from the rhizosphere, rice roots rely on two Fe acquisition pathways. The first of these pathways involves Fe(III) chelators specific to graminaceous plants, the mugineic acid family phytosiderophores, and the second involves absorption of Fe(2+). Key components in this response include enzymes involved in the biosynthesis of deoxymugineic acid (OsNAS1, OsNAS2, OsNAAT1, and OsDMAS1), the deoxymugineic acid efflux transporter (TOM1), the Fe(III)-deoxymugineic acid transporter (OsYSL15), and Fe(2+) transporters (OsIRT1, OsIRT2, and OsNRAMP1). In whole roots, these proteins are expressed in a coordinated manner with strong transcriptional induction in response to Fe deficiency. Radial transport of Fe to xylem and phloem is also mediated by the mugineic acid family phytosiderophores, as well as other chelators and their transporters, including Fe(II)-nicotianamine transporter (OsYSL2), phenolics efflux transporters (PEZ1 and PEZ2), and citrate efflux transporter (OsFRDL1). Among these, OsYSL2 is strongly induced under conditions of Fe deficiency. Both transcriptional induction and potential feedback repression mediate the expressional regulation of the genes involved in Fe uptake and translocation in response to Fe deficiency. The transcription factors IDEF1, IDEF2, and OsIRO2 are responsible for transcriptional induction, whereas the ubiquitin ligases OsHRZ1 and OsHRZ2, as well as the transcription factors OsIRO3 and OsbHLH133, are thought to mediate negative regulation. Furthermore, IDEF1 and OsHRZs bind Fe and other metals, and are therefore candidate Fe sensors. The interacting functions of these regulators are thought to fine tune the expression of proteins involved in Fe uptake and translocation.

Tissue-specific transcriptional profiling of iron-deficient and cadmium-stressed rice using laser capture microdissection

Several metals are essential nutrients for plants. However, they become toxic at high levels and deleteriously affect crop yield and quality. We recently reported the spatial gene expression profiles of iron (Fe)-deficient and cadmium (Cd)-stressed rice using laser microdissection and microarray analysis. The roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately (newDC and oldDC, respectively). Genes expressed in a tissue-specific manner in the VB, Cor, EP, newDC, and oldDC formed large clusters. The genes upregulated in all of the VB, Cor, and EP by Fe deficiency formed a substantial cluster that was smaller than the tissue-specific clusters. Significant numbers of genes expressed in newDC or oldDC were also expressed in VB in roots, suggesting that vascular bundles in the lowest nodes and roots have a partially common function. The expression patterns of transporter families involved in metal homeostasis were investigated, and members of each family were either expressed differentially in each tissue or showed different responses to Fe deficiency. One potassium transporter gene, OsHAK22, was upregulated by Fe deficiency in VB, Cor, and EP, suggesting that OsHAK22 is involved in potassium transport associated with mugineic acids secretion.