Increased root hair density by loss of WRKY6 in Arabidopsis thaliana

Genome-wide identification of WRKY transcription factors in Casuarina equisetifolia and the function analysis of CeqWRKY11 in response to NaCl/NaHCO3 stresses

BACKGROUND

Casuarina equisetifolia (C. equisetifolia) is a woody species with many excellent features. It has natural resistance against drought, salt and saline-alkali stresses. WRKY transcription factors (TFs) play significant roles in plant response to abiotic stresses, therefore, molecular characterization of WRKY gene family under abiotic stresses holds great significance for improvement of forest trees through molecular biological tools. At present, WRKY TFs from C. equisetifolia have not been thoroughly studied with respect to their role in salt and saline-alkali stresses response. The current study was conducted to bridge the same knowledge gap.

RESULTS

A total of 64 WRKYs were identified in C. equisetifolia and divided into three major groups i.e. group I, II and III, consisting of 10, 42 and 12 WRKY members, respectively. The WRKY members in group II were further divided into 5 subgroups according to their homology with Arabidopsis counterparts. WRKYs belonging to the same group exhibited higher similarities in gene structure and the presence of conserved motifs. Promoter analysis data showed the presence of various response elements, especially those related to hormone signaling and abiotic stresses, such as ABRE (ABA), TGACG (MeJA), W-box ((C/T) TGAC (T/C)) and TC-rich motif. Tissue specific expression data showed that CeqWRKYs were mainly expressed in root under normal growth conditions. Furthermore, most of the CeqWRKYs were up-regulated by NaCl and NaHCO3 stresses with few of WRKYs showing early responsiveness to both stresses while few others exhibiting late response. Although the expressions of CeqWRKYs were also induced by cold stress, the response was delayed compared with other stresses. Transgenic C. equisetifolia plants overexpressing CeqWRKY11 displayed lower electrolyte leakage, higher chlorophyll content, and enhanced tolerance to both stresses. The higher expression of abiotic stress related genes, especially CeqHKT1 and CeqPOD7, in overexpression lines points to the maintenance of optimum Na+/K+ ratio, and ROS scavenging as possible key molecular mechanisms underlying salt stress tolerance.

CONCLUSIONS

Our results show that CeqWRKYs might be key regulators of NaCl and NaHCO3 stresses response in C. equisetifolia. In addition, positive correlation of CeqWRKY11 expression with increased stress tolerance in C. equisetifolia encourages further research on other WRKY family members through functional genomic tools. The best candidates could be incorporated in other woody plant species for improving stress tolerance.

The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status

Phosphate (P_i ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of P_i . The mechanisms to cope with P_i limitation as well as direct uptake of P_i from the substrate via the root epidermis are regulated by a conserved P_i starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain P_i indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for P_i . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant P_i uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.

Strigolactone regulates adventitious root formation via the MdSMXL7-MdWRKY6-MdBRC1 signaling cascade in apple

Propagation through stem cuttings is a popular method worldwide for species such as fruit tree rootstocks and forest trees. Adventitious root (AR) formation from stem cuttings is crucial for effective and successful clonal propagation of apple rootstocks. Strigolactones (SLs) are newly identified hormones involved in AR formation. However, the regulatory mechanisms underpinning this process remain elusive. In the present study, weighted gene co-expression network analysis, as well as rooting assays using stable transgenic apple materials, revealed that MdBRC1 served as a key gene in the inhibition of AR formation by SLs. We have demonstrated that MdSMXL7 and MdWRKY6 synergistically regulated MdBRC1 expression, depending on the interactions of MdSMXL7 and MdWRKY6 at the protein level downstream of SLs as well as the direct promoter binding on MdBRC1 by MdWRKY6. Furthermore, biochemical studies and genetic analysis revealed that MdBRC1 inhibited AR formation by triggering the expression of MdGH3.1 in a transcriptional activation pathway. Finally, the present study not only proposes a component, MdWRKY6, that enables MdSMXL7 to regulate MdBRC1 during the process of SL-controlled AR formation in apple, but also provides prospective target genes to enhance AR formation capacity using CRISPR (i.e. clustered regularly interspaced short palindromic repeats) technology, particularly in woody plants.

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.

Stimulation of photosynthesis and enhancement of growth and yield in Arabidopsis thaliana treated with amine-functionalized mesoporous silica nanoparticles

Mesoporous silica nanoparticles (MSNs) of 50 nm diameter particle size with a pore size of approximately 14.7 nm were functionalized with amino groups (Am-MSNs) and the effects of exposure to these positively charged Am-MSNs on each of the life cycle stages of Arabidopsis thaliana were investigated. After growth in half strength MS medium amended with Am-MSNs (0-100 μg/mL) for 7 and 14 days, seed germination rate and seedling growth were significantly increased compared with untreated controls. The seedlings were then transferred to soil and irrigated with Am-MSNs solutions every 3 days until seed harvesting. After four weeks growth in soil, Am-MSNs treated plants showed up-regulation of chlorophyll and carotenoid synthesis-related genes, an increase in the content of photosynthetic pigments and an amplification of plant photosynthetic capacity. All these changes in plants were closely correlated with greater vegetative growth and higher seed yield. In all the experiments, 20 and 50 μg/mL of Am-MSNs were found to be more effective with respect to other treatments, while Am-MSNs at the highest level of 100 μg/mL did not result in oxidative stress or cell membrane damage in the exposed plants. To the best of our knowledge, this is the first report evaluating both physiological and molecular responses following exposure to plants of these specific Am-MSNs throughout their whole life cycle. Overall, these findings indicate that following exposure Am-MSNs play a major role in the increase in seed germination, biomass, photosynthetic pigments, photosynthetic capacity and seed yield in A. thaliana.

Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses

BACKGROUND

Cucumber (Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern of WRKY genes under different stresses in cucumber.

RESULTS

In the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumber WRKY genes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumber WRKY genes. The 61 CsWRKYs were classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of the WRKY genes demonstrated that 24 CsWRKY genes showed constitutive expression (FPKM > 1 in all samples), and some WRKY genes showed organ-specific expression, suggesting that these WRKYs might be important for plant growth and organ development in cucumber. Importantly, analysis of the CsWRKY gene expression patterns revealed that five CsWRKY genes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and three CsWRKY genes simultaneously responded to all treatments analysed. Some CsWRKY genes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumber WRKY genes might play different roles during different stress responses and that their expression patterns vary in response to stresses.

CONCLUSIONS

Sixty-one WRKY genes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function of CsWRKY genes in improving abiotic and biotic stress resistance in cucumber.

Identifying key regulatory genes of maize root growth and development by RNA sequencing

Root system architecture (RSA), the spatio-temporal configuration of roots, plays vital roles in maize (Zea mays L.) development and productivity. We sequenced the maize root transcriptome of four key growth and development stages: the 6th leaf stage, the 12th leaf stage, the tasseling stage and the milk-ripe stage. Differentially expressed genes (DEGs) were detected. 81 DEGs involved in plant hormone signal transduction pathway and 26 transcription factor (TF) genes were screened. These DEGs and TFs were predicted to be potential candidate genes during maize root growth and development. Several of these genes are homologous to well-known genes regulating root architecture or development in Arabidopsis or rice, such as, Zm00001d005892 (AtERF109), Zm00001d027925 (AtERF73/HRE1), Zm00001d047017 (AtMYC2, OsMYC2), Zm00001d039245 (AtWRKY6). Identification of these key genes will provide a further understanding of the molecular mechanisms responsible for maize root growth and development, it will be beneficial to increase maize production and improve stress resistance by altering RSA traits in modern breeding.

The WRKY6 transcription factor affects seed oil accumulation and alters fatty acid compositions in Arabidopsis thaliana

In rapeseed, the oil content of the seed not only supplies energy for seed germination and seedling development but also provides essential dietary nutrients for humans and livestock. Recent studies have revealed that many transcription factors (TFs) regulate the accumulation of fatty acids (FAs) during seed development. WRKY6, a WRKY6 family TF, was reported to serve a function in the plant senescence processes, pathogen defense mechanisms and abiotic stress responses. However, the precise role of WRKY6 in influencing FA accumulation in seeds is still unknown. In this study, we demonstrate that WRKY6 has a high expression level in developing seeds and plays an essential role in regulating the accumulation of FAs in developing seeds of Arabidopsis. Mutation of WRKY6 resulted in significant increase in seed size, accompanied by an increase in FA content and changes in FA composition. Ultrastructure analyses showed that the absence of WRKY6 resulted in more and higher percentage of oil body in the cell of mature seeds. Quantitative real-time PCR analysis revealed changes in the expression of several genes related to photosynthesis and FA biosynthesis in wrky6 mutants at 10 or 16 days after pollination. These results reveal a novel function of WRKY6 influencing seed oil content and FAs compositions. This gene could be used as a promising gene resource to improve FA accumulation and seed yield in Brassica napus through genetic manipulation.

Ethylene and Phloem Signals Are Involved in the Regulation of Responses to Fe and P Deficiencies in Roots of Strategy I Plants

Iron (Fe) and phosphorus (P) are two essential mineral nutrients whose acquisition by plants presents important environmental and economic implications. Both elements are abundant in most soils but scarcely available to plants. To prevent Fe or P deficiency dicot plants initiate morphological and physiological responses in their roots aimed to specifically acquire these elements. The existence of common signals in Fe and P deficiency pathways suggests the signaling factors must act in conjunction with distinct nutrient-specific signals in order to confer tolerance to each deficiency. Previous works have shown the existence of cross talk between responses to Fe and P deficiency, but details of the associated signaling pathways remain unclear. Herein, the impact of foliar application of either P or Fe on P and Fe responses was studied in P- or Fe-deficient plants of Arabidopsis thaliana, including mutants exhibiting altered Fe or P homeostasis. Ferric reductase and acid phosphatase activities in roots were determined as well as the expression of genes related to P and Fe acquisition. The results obtained showed that Fe deficiency induces the expression of P acquisition genes and phosphatase activity, whereas P deficiency induces the expression of Fe acquisition genes and ferric reductase activity, although only transitorily. Importantly, these responses were reversed upon foliar application of either Fe or P on nutrient-starved plants. Taken together, the results reveal interactions between P- and Fe-related phloem signals originating in the shoots that likely interact with hormones in the roots to initiate adaptive mechanisms to tolerate deficiency of each nutrient.

Root hairs enhance Arabidopsis seedling survival upon soil disruption

Root hairs form a substantial portion of the root surface area. Compared with their nutritional function, the physical function of root hairs has been poorly characterised. This study investigates the physical role of root hairs of Arabidopsis thaliana seedlings in interaction of the root with water and soil and in plant survival upon soil disruption. Five transgenic lines with different root hair lengths were used to assess the physical function of root hairs. Upon soil disruption by water falling from a height (mimicking rainfall), long-haired lines showed much higher anchorage rates than short-haired lines. The root-pulling test revealed that a greater amount of soil adhered to long-haired roots than to short-haired roots. When seedlings were pulled out and laid on the soil surface for 15 d, survival rates of long-haired seedlings were higher than those of short-haired seedlings. Moreover, the water holding capacity of roots was much greater among long-haired seedlings than short-haired seedlings. These results suggest that root hairs play a significant role in plant survival upon soil disruption which could be fatal for young seedlings growing on thin soil surface with a short primary root and root hairs as the only soil anchoring system.

Similarities and Differences in the Acquisition of Fe and P by Dicot Plants

This review deals with two essential plant mineral nutrients, iron (Fe) and phosphorus (P); the acquisition of both has important environmental and economic implications. Both elements are abundant in soils but are scarcely available to plants. To prevent deficiency, dicot plants develop physiological and morphological responses in their roots to specifically acquire Fe or P. Hormones and signalling substances, like ethylene, auxin and nitric oxide (NO), are involved in the activation of nutrient-deficiency responses. The existence of common inducers suggests that they must act in conjunction with nutrient-specific signals in order to develop nutrient-specific deficiency responses. There is evidence suggesting that P- or Fe-related phloem signals could interact with ethylene and NO to confer specificity to the responses to Fe- or P-deficiency, avoiding their induction when ethylene and NO increase due to other nutrient deficiency or stress. The mechanisms responsible for such interaction are not clearly determined, and thus, the regulatory networks that allow or prevent cross talk between P and Fe deficiency responses remain obscure. Here, fragmented information is drawn together to provide a clearer overview of the mechanisms and molecular players involved in the regulation of the responses to Fe or P deficiency and their interactions.

CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production

As the world population increases, strategies for sustainable agriculture are needed to fulfill the global need for plants for food and other commercial products. Nanoparticle formulations are likely to be part of the developing strategies. CuO and ZnO nanoparticles (NPs) offer potential as fertilizers, as they provide bioavailable essential metals, and as pesticides, because of dose-dependent toxicity. Effects of these metal oxide NPs on rhizosphere functions are the focus of this review. These NPs at doses of ≥10 mg metal/kg change the production of key metabolites involved in plant protection in a root-associated microbe, Pseudomonas chlororaphis O6. Altered synthesis occurs in the microbe for phenazines, which function in plant resistance to pathogens, the pyoverdine-like siderophore that enhances Fe bioavailability in the rhizosphere and indole-3-acetic acid affecting plant growth. In wheat seedlings, reprogramming of root morphology involves increases in root hair proliferation (CuO NPs) and lateral root formation (ZnO NPs). Systemic changes in wheat shoot gene expression point to altered regulation for metal stress resilience as well as the potential for enhanced survival under stress commonly encountered in the field. These responses to the NPs cross kingdoms involving the bacteria, fungi, and plants in the rhizosphere. Our challenge is to learn how to understand the value of these potential changes and successfully formulate the NPs for optimal activity in the rhizosphere of crop plants. These formulations may be integrated into developing practices to ensure the sustainability of crop production.

Adaptation of Arabidopsis thaliana to the Yangtze River basin

Background

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different.

Results

We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping.

Conclusions

A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.

Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency

BACKGROUND

Deficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions.

METHODS

Four oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic-KH2PO4 (control), organic-phytate (PA) and with no phosphate (-P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed.

RESULTS

All studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform pattern was similar in all studied conditions, usually with a higher level of one of the isoforms under Pi starvation. Generally no significant effects of mycorrhizal colonization on growth of oat cultivars were observed.

DISCUSSION

We postulated that acid phosphatases played the most important role in oat cultivars acclimation to Pi deficiency, especially extracellular enzymes involved in Pi acquisition from soil organic P esters. These APases are mainly located in the epidermis of young roots, and may be released to the rhizosphere. On the other hand, intracellular APases could be involved in fast Pi remobilization from internal sources. Our study showed that oat, in contrast to other plants, can use phytates as the sole source of P. The studied oat cultivars demonstrated similar acclimation mechanisms to Pi deficiency, however, depending on stress level, they can use different pools of acid phosphatases.