SNF1-related protein kinases type 2 are involved in plant responses to cadmium stress

Protein kinase SnRK2.4 is a key regulator of aquaporins and root hydraulics in Arabidopsis

Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever-changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; Lpr ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to Lpr . Using recombinant lines from a biparental cross (Cvi-0 x Col-0), we show that the gene encoding class 2 Sucrose-Non-Fermenting Protein kinase 2.4 (SnRK2.4) in Col-0 contributes to >30% of Lpr by enhancing aquaporin-dependent water transport. At variance with the inactive and possibly unstable Cvi-0 SnRK2.4 form, the Col-0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col-0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long-term (>3 h) inhibition of Lpr by ABA possibly involves a SnRK2.4-independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA-induced inhibition of primary root growth. The study identifies a key component of Lpr and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA-dependent or independent SnRK2s.

SnRK2.10 kinase differentially modulates expression of hub WRKY transcription factors genes under salinity and oxidative stress in Arabidopsis thaliana

In nature, all living organisms must continuously sense their surroundings and react to the occurring changes. In the cell, the information about these changes is transmitted to all cellular compartments, including the nucleus, by multiple phosphorylation cascades. Sucrose Non-Fermenting 1 Related Protein Kinases (SnRK2s) are plant-specific enzymes widely distributed across the plant kingdom and key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress and salinity. The main deleterious effects of salinity comprise water deficiency stress, disturbances in ion balance, and the accompanying appearance of oxidative stress. The reactive oxygen species (ROS) generated at the early stages of salt stress are involved in triggering intracellular signaling required for the fast stress response and modulation of gene expression. Here we established in Arabidopsis thaliana that salt stress or induction of ROS accumulation by treatment of plants with H2O2 or methyl viologen (MV) induces the expression of several genes encoding transcription factors (TFs) from the WRKY DNA-Binding Protein (WRKY) family. Their induction by salinity was dependent on SnRK2.10, an ABA non-activated kinase, as it was strongly reduced in snrk2.10 mutants. The effect of ROS was clearly dependent on their source. Following the H2O2 treatment, SnRK2.10 was activated in wild-type (wt) plants and the induction of the WRKY TFs expression was only moderate and was enhanced in snrk2.10 lines. In contrast, MV did not activate SnRK2.10 and the WRKY induction was very strong and was similar in wt and snrk2.10 plants. A bioinformatic analysis indicated that the WRKY33, WRKY40, WRKY46, and WRKY75 transcription factors have a similar target range comprising numerous stress-responsive protein kinases. Our results indicate that the stress-related functioning of SnRK2.10 is fine-tuned by the source and intracellular distribution of ROS and the co-occurrence of other stress factors.

The TabHLH35-TaWAK20-TaSPL5 pathway positively regulates Cd stress in wheat

KEY MESSAGE

Cadmium-induced TaWAK20 regulates the cadmium stress response by phosphorylating TaSPL5 in wheat. Receptor-like kinases (RLKs) are thought to play important roles in responses to abiotic stresses in plants. In this study, we identified a cadmium (Cd)-induced RLK in wheat, TaWAK20, which is a positive regulator of the Cd stress response. TaWAK20 is specifically expressed in root tissue. Overexpression of TaWAK20 significantly improved the tolerance of Cd stress in wheat and decreased Cd accumulation in wheat plants by regulating reactive oxygen species production and scavenging. Yeast one-hybrid assays, electrophoretic mobility shift assays, and firefly luciferase activity analyses demonstrated that the TaWAK20 promoter was bound by the TabHLH35 transcription factor. TaWAK20 interacted with and phosphorylated squamosa promoter binding protein-like 5 (TaSPL5). Furthermore, phosphorylation of TaSPL5 increased its DNA-binding activity. In addition, Arabidopsis-expressing phosphorylated TaSPL5 exhibited greater Cd tolerance than Arabidopsis-expressing unphosphorylated TaSPL5. Taken together, these data identify a TabHLH35-TaWAK20-TaSPL5 module that regulates Cd stress.

Arabidopsis SUMO E3 ligase SIZ1 enhances cadmium tolerance via the glutathione-dependent phytochelatin synthesis pathway

Sumoylation is a posttranslational modification (PTM) in which SUMO (small ubiquitin-like modifier) is covalently conjugated to protein substrates via a range of enzymes. SUMO E3 ligase SIZ1 is involved in mediating several essential or nonessential element-responsive SUMO conjugations in Arabidopsis. However, whether SIZ1 is involved in the cadmium (Cd) response remains to be identified. In this study, we found that SIZ1 positively regulates plant Cd tolerance. The loss-of-function siz1-2 mutant exhibited impaired resistance to Cd exposure and accumulated more reactive oxygen species (ROS). Moreover, the transcription of GSH1, GSH2, PCS1, and PCS2 was suppressed while the accumulation of Cd was enhanced in the siz1-2 mutant under Cd exposure. Further analysis revealed that the higher Cd sensitivity of the siz1-2 mutant was partially rescued by the overexpression of GSH1. Consistently, Cd stress stimulated the accumulation of SUMO1 conjugates in wild-type plants but not in the siz1-2 mutant. Together, our results demonstrate that Cd-induced SIZ1 activates GSH- and PC synthesis-related gene expression to increase the synthesis of GSH- and PCs, thereby leading to higher Cd tolerance in plants.

To grow or not to grow under nutrient scarcity: Target of rapamycin-ethylene is the question

To cope with nutrient scarcity, plants generally follow two main complementary strategies. On the one hand, they can slow down growing, mainly shoot growth, to diminish the demand of nutrients. We can call this strategy as "stop growing." On the other hand, plants can develop different physiological and morphological responses, mainly in their roots, aimed to facilitate the acquisition of nutrients. We can call this second strategy as "searching for nutrients." Both strategies are compatible and can function simultaneously but the interconnection between them is not yet well-known. In relation to the "stop growing" strategy, it is known that the TOR (Target Of Rapamycin) system is a central regulator of growth in response to nutrients in eukaryotic cells. TOR is a protein complex with kinase activity that promotes protein synthesis and growth while some SnRK (Sucrose non-fermenting 1-Related protein Kinases) and GCN (General Control Non-derepressible) kinases act antagonistically. It is also known that some SnRKs and GCNs are activated by nutrient deficiencies while TOR is active under nutrient sufficiency. In relation to the "searching for nutrients" strategy, it is known that the plant hormone ethylene participates in the activation of many nutrient deficiency responses. In this Mini Review, we discuss the possible role of ethylene as the hub connecting the "stop growing" strategy and the "searching for nutrients" strategy since very recent results also suggest a clear relationship of ethylene with the TOR system.

Red and blue light function antagonistically to regulate cadmium tolerance by modulating the photosynthesis,antioxidant defense system and Cd uptake in cucumber(Cucumis sativus L.)

Cadmium (Cd) is highly toxic to both plants and humans.Light plays crucial roles in plant growth, development and stress responses, but how light functions in plant Cd response remain unclear.Here,we found that Cd treatment significantly induced the expression of PHYB but not PHYA and CRY1 in leaves and roots of cucumber. Correspondingly,compared with white light (W) during Cd stress,red light(R) increased Cd sensitivity,whereas blue light (B) enhanced Cd tolerance as evidenced by decreased Cd-induced chlorosis, growth inhibition, photosynthesis inhibition and chloroplast ultrastructure damage.Furthermore,B markedly increased the transcripts and activities of the antioxidant enzymes including ascorbate peroxidase (APX),catalase (CAT),superoxide dismutase (SOD) and glutathione reductase (GR),as well as glutathione (GSH) content and GSH1 expression, resulting in hydrogen peroxide (H₂O₂) and superoxide (O₂^.-) reduction,but R treatment showed the opposite trend. Moreover, R and B markedly up-regulated and down-regulated the expression levels of Cd uptake and transport genes including IRT1, NRAMP1 and HMA3, leading to more and less Cd accumulation than the W-treated plants in both shoots and roots, respectively under Cd stress. Collectively, our data clearly demonstrate that R and B function antagonistically to regulate Cd tolerance in cucumber via modulating the photosynthesis, antioxidant defense system and Cd uptake, providing a novel light quality control strategy to enhance crop Cd tolerance and food safety.

Stress signaling convergence and nutrient crosstalk determine zinc-mediated amelioration against cadmium toxicity in rice

Consumption of rice (Oryza sativa L.) is one of the major pathways for heavy metal bioaccumulation in humans over time. Understanding the molecular responses of rice to heavy metal contamination in agriculture is useful for eco-toxicological assessment of cadmium (Cd) and its interaction with zinc (Zn). In certain crops, the impacts of Cd stress or Zn nutrition on the biophysical chemistry and gene expression have been widely investigated, but their molecular interactions at transcriptomic level, particularly in rice roots, are still elusive. Here, hydroponic investigations were carried out with two rice genotypes (Yinni-801 and Heizhan-43), varying in Cd contents in plant tissues to determine their transcriptomic responses upon Cd15 (15 µM) and Cd15+Zn50 (50 µM) treatments. High throughput RNA-sequencing analysis confirmed that 496 and 2407 DEGs were significantly affected by Cd15 and Cd15+Zn50, respectively, among which 1016 DEGs were commonly induced in both genotypes. Multitude of DEGs fell under the category of protein kinases, such as calmodulin (CaM) and calcineurin B-like protein-interacting protein kinases (CBL), indicating a dynamic shift in hormonal signal transduction and Ca2+ involvement with the onset of treatments. Both genotypes expressed a mutual regulation of transcription factors (TFs) such as WRKY, MYB, NAM, AP2, bHLH and ZFP families under both treatments, whereas genes econding ABC transporters (ABCs), high affinity K+ transporters (HAKs) and Glutathione-S-transferases (GSTs), were highly up-regulated under Cd15+Zn50 in both genotypes. Zinc addition triggered more signaling cascades and detoxification related genes in regulation of immunity along with the suppression of Cd-induced DEGs and restriction of Cd uptake. Conclusively, the effective integration of breeding techniques with candidate genes identified in this study as well as economically and technologically viable methods, such as Zn nutrient management, could pave the way for selecting cultivars with promising agronomic qualities and reduced Cd for sustainable rice production.

The SnRK2.10 kinase mitigates the adverse effects of salinity by protecting photosynthetic machinery

SNF1-Related protein kinases Type 2 (SnRK2) are plant-specific enzymes widely distributed across the plant kingdom. They are key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress. Here we established that SnRK2.4 and SnRK2.10, ABA-nonactivated kinases, are activated in Arabidopsis thaliana rosettes during the early response to salt stress and contribute to leaf growth retardation under prolonged salinity but act by maintaining different salt-triggered mechanisms. Under salinity, snrk2.10 insertion mutants were impaired in the reconstruction and rearrangement of damaged core and antenna protein complexes in photosystem II (PSII), which led to stronger non-photochemical quenching, lower maximal quantum yield of PSII, and lower adaptation of the photosynthetic apparatus to high light intensity. The observed effects were likely caused by disturbed accumulation and phosphorylation status of the main PSII core and antenna proteins. Finally, we found a higher accumulation of reactive oxygen species (ROS) in the snrk2.10 mutant leaves under a few-day-long exposure to salinity which also could contribute to the stronger damage of the photosynthetic apparatus and cause other deleterious effects affecting plant growth. We found that the snrk2.4 mutant plants did not display substantial changes in photosynthesis. Overall, our results indicate that SnRK2.10 is activated in leaves shortly after plant exposure to salinity and contributes to salt stress tolerance by maintaining efficient photosynthesis and preventing oxidative damage.

The Multifaceted Regulation of SnRK2 Kinases

SNF1-related kinases 2 (SnRK2s) are central regulators of plant responses to environmental cues simultaneously playing a pivotal role in the plant development and growth in favorable conditions. They are activated in response to osmotic stress and some of them also to abscisic acid (ABA), the latter being key in ABA signaling. The SnRK2s can be viewed as molecular switches between growth and stress response; therefore, their activity is tightly regulated; needed only for a short time to trigger the response, it has to be induced transiently and otherwise kept at a very low level. This implies a strict and multifaceted control of SnRK2s in plant cells. Despite emerging new information concerning the regulation of SnRK2s, especially those involved in ABA signaling, a lot remains to be uncovered, the regulation of SnRK2s in an ABA-independent manner being particularly understudied. Here, we present an overview of available data, discuss some controversial issues, and provide our perspective on SnRK2 regulation.

Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis

SWI/SNF chromatin remodelers are evolutionarily conserved multiprotein complexes that use the energy of ATP hydrolysis to change chromatin structure. A characteristic feature of SWI/SNF remodelers is the occurrence in both the catalytic ATPase subunit and some auxiliary subunits, of bromodomains, the protein motifs capable of binding acetylated histones. Here, we report that the Arabidopsis bromodomain-containing proteins BRD1, BRD2, and BRD13 are likely true SWI/SNF subunits that interact with the core SWI/SNF components SWI3C and SWP73B. Loss of function of each single BRD protein caused early flowering but had a negligible effect on other developmental pathways. By contrast, a brd triple mutation (brdx3) led to more pronounced developmental abnormalities, indicating functional redundancy among the BRD proteins. The brdx3 phenotypes, including hypersensitivity to abscisic acid and the gibberellin biosynthesis inhibitor paclobutrazol, resembled those of swi/snf mutants. Furthermore, the BRM protein level and occupancy at the direct target loci SCL3, ABI5, and SVP were reduced in the brdx3 mutant background. Finally, a brdx3 brm-3 quadruple mutant, in which SWI/SNF complexes were devoid of all constituent bromodomains, phenocopied a loss-of-function mutation in BRM. Taken together, our results demonstrate the relevance of BRDs as SWI/SNF subunits and suggest their cooperation with the bromodomain of BRM ATPase.

Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation

Cadmium is a toxic metal widely found in workplaces and plant soil because of extensive industrialization. Wheat is an important source of food generated from plant soil. The different responses of wheat against different omic levels of cadmium have been observed and widely studied worldwide. With the development of high-throughput sequencing, micro-level biological research has extended to the microRNA level. In this study, high-cadmium-accumulating wheat cultivars (Annong9267) and low-cadmium-accumulating wheat cultivars (Qian 102032) were used as experimental models. The two cultivars were treated by Cd for 2 h to explore the microRNA profiles in root and leaf tissues through small RNA sequencing. Important small RNAs, such as tae-miR9663-5p and tae-miR6201, and potential small RNA-mediated mechanisms associated with cadmium accumulation were identified by summarizing specific microRNA profiling patterns and their respective target genes. At the wheat roots and leaves, differentially expressed small RNAs related to cadmium accumulation in different plant tissues (roots or leaves) were identified, and functional enrichment analyses on target genes of differentially expressed miRNAs in low- and high-cadmium-accumulating wheat cultivars in different plant tissues (roots or leaves) obtained some known mature miRNAs and new miRNAs. The identified miRNA will be regarded as a potential screening biomarker for low-cadmium-accumulating wheat.

Cellular Phosphorylation Signaling and Gene Expression in Drought Stress Responses: ABA-Dependent and ABA-Independent Regulatory Systems

Drought is a severe and complex abiotic stress that negatively affects plant growth and crop yields. Numerous genes with various functions are induced in response to drought stress to acquire drought stress tolerance. The phytohormone abscisic acid (ABA) accumulates mainly in the leaves in response to drought stress and then activates subclass III SNF1-related protein kinases 2 (SnRK2s), which are key phosphoregulators of ABA signaling. ABA mediates a wide variety of gene expression processes through stress-responsive transcription factors, including ABA-RESPONSIVE ELEMENT BINDING PROTEINS (AREBs)/ABRE-BINDING FACTORS (ABFs) and several other transcription factors. Seed plants have another type of SnRK2s, ABA-unresponsive subclass I SnRK2s, that mediates the stability of gene expression through the mRNA decay pathway and plant growth under drought stress in an ABA-independent manner. Recent research has elucidated the upstream regulators of SnRK2s, RAF-like protein kinases, involved in early responses to drought stress. ABA-independent transcriptional regulatory systems and ABA-responsive regulation function in drought-responsive gene expression. DEHYDRATION RESPONSIVE ELEMENT (DRE) is an important cis-acting element in ABA-independent transcription, whereas ABA-RESPONSIVE ELEMENT (ABRE) cis-acting element functions in ABA-responsive transcription. In this review article, we summarize recent advances in research on cellular and molecular drought stress responses and focus on phosphorylation signaling and transcription networks in Arabidopsis and crops. We also highlight gene networks of transcriptional regulation through two major regulatory pathways, ABA-dependent and ABA-independent pathways, that ABA-responsive subclass III SnRK2s and ABA-unresponsive subclass I SnRK2s mediate, respectively. We also discuss crosstalk in these regulatory systems under drought stress.

The Arabidopsis sucrose non-fermenting-1-related protein kinase AtSnRK2.4 interacts with a transcription factor, AtMYB21, that is involved in salt tolerance

Sucrose non-fermenting-1-related protein kinase 2 s (SnRK2 s) are important stress-related plant protein kinases in plants. The interaction partners and phosphorylation substrates of group II and III SnRK2 s in Arabidopsis thaliana have been identified, but similar data for group I SnRK2 s are very limited. Here, we used a yeast two-hybrid (Y2H) screen to find proteins that interact with Arabidopsis AtSnRK2.4, a group I SnRK2. The transcription factor AtMYB21 was identified as an AtSnRK2.4 interaction partner, and its interaction with AtSnRK2.4 was confirmed by an in vitro pull-down assay and a bimolecular fluorescence complementation (BiFC) assay. A subcellular localization assay demonstrated that AtSnRK2.4 and AtMYB21 were located in the cytoplasm and nucleus of onion epidermal cells. AtSnRK2.4 and AtMYB21 were expressed in many tissues and upregulated in response to NaCl stress. Transgenic plants that overexpressed AtSnRK2.4 or AtMYB21 gene exhibited enhanced tolerance to salt stress at germination and post-germination stages. Moreover, the expression of downstream stress-responsive genes was upregulated in salt-stressed AtSnRK2.4 and AtMYB21 transgenic Arabidopsis. These results suggest that AtSnRK2.4 may act synergistically with AtMYB21 to mediate the response to salt stress through the upregulation of downstream stress-responsive genes.

The kinase CIPK11 functions as a positive regulator in cadmium stress response in Arabidopsis

Cadmium (Cd) pollution in agricultural soil has always been a knotty problem, which made it necessary to find the mechanism related to Cd transport in plant. In this study, we found a novel character of the CIPK11 modulating the transport of Cd in Arabidopsis thaliana. Over-expression of CIPK11 (CIPK11OE#1-7, CIPK11OE#8-5) resulted in the increased tolerance to Cd stress, which embodied in higher fresh weight, lower Cd enrichment and reactive oxygen species (ROS) than the wild-type (WT) plants. qRT-PCR results showed a collective down-regulation of the expression of IRT1 and transcription factor genes FIT, bHLH039 in the CIPK11-overexpression plants after Cd stress. Overexpression of CIPK11 significantly increased the expression of ABA marker genes in Arabidopsis after Cd stress. With different concentrations of ABA treatment, the root length differences caused by Cd stress could be recovered. However the transcription levels of FIT and bHLH039 decreased in WT and cipk11 mutant when treated with ABA which indicated that ABA can inhibit the transcription of IRT1 by repressing FIT and bHLH039 expression. Taken together, our results demonstrated that the kinase CIPK11 responses to Cd stress by ABA signaling pathway.

Decoding Heavy Metal Stress Signalling in Plants: Towards Improved Food Security and Safety

The mining of heavy metals from the environment leads to an increase in soil pollution, leading to the uptake of heavy metals into plant tissue. The build-up of toxic metals in plant cells often leads to cellular damage and senescence. Therefore, it is of utmost importance to produce plants with improved tolerance to heavy metals for food security, as well as to limit heavy metal uptake for improved food safety purposes. To achieve this goal, our understanding of the signaling mechanisms which regulate toxic heavy metal uptake and tolerance in plants requires extensive improvement. In this review, we summarize recent literature and data on heavy metal toxicity (oral reference doses) and the impact of the metals on food safety and food security. Furthermore, we discuss some of the key events (reception, transduction, and response) in the heavy metal signaling cascades in the cell wall, plasma membrane, and cytoplasm. Our future perspectives provide an outlook of the exciting advances that will shape the plant heavy metal signaling field in the near future.

Quantitative proteomic analysis reveals complex regulatory and metabolic response of Iris lactea Pall. var. chinensis to cadmium toxicity

Cadmium pollution has become a serious environmental problem. Iris lactea var. chinensis showed strong Cd tolerance and accumulation ability, which has significant potential to be applied for the phytoremediation of Cd-contaminated soil. However, the lack of molecular information on the mechanism of I. lactea response to Cd limited the improvement of phytoremediation efficiency. In this study, label-free proteomics analysis of Cd response in I. lactea showed that there were 163 and 196 differentially expressed proteins (DEPs) in the shoots and roots, respectively. Bioinformatics analysis indicated the DEPs responding to Cd stress mainly involved in signal transduction, ion transport, redox etc., and participate in the pathway of amino acid biosynthesis, lignin biosynthesis, glycerolipid metabolism and glutathione metabolism. Besides, differential expression of seven DEPs was validated via gene expression analysis. Finally, we found that a Cd-induced mannose-specific lectin (IlMSL) from I. lactea enhanced the Cd sensitivity and increased Cd accumulation in yeast. The results of this study will enhance our understanding of the molecular mechanism of Cd tolerance and accumulation in I. lactea and ultimately provide valuable resources for using Cd tolerant genes for developing efficient strategies for phytoremediation of Cd-contaminated soils or limiting Cd accumulation in food crops.

Regulation of ABA-Non-Activated SNF1-Related Protein Kinase 2 Signaling Pathways by Phosphatidic Acid

Phosphatidic acid (PA) is involved in the regulation of plant growth and development, as well as responses to various environmental stimuli. Several PA targets in plant cells were identified, including two SNF1-related protein kinases 2 (SnRK2s), SnRK2.10 and SnRK2.4, which are not activated by abscisic acid (ABA). Here, we investigated the effects of PA on various elements of ABA-non-activated SnRK2 signaling. PA 16:0/18:1 was found to modulate the SnRK2 structure and the phosphorylation of some SnRK2 targets. Conversely, phosphorylation by the ABA-non-activated SnRK2s, of one of such targets, dehydrin Early Responsive to Dehydration 14 (ERD14), affects its interaction with PA and subcellular localization. Moreover, PA 16:0/18:1 modulates the activity and/or localization of negative regulators of the ABA-non-activated SnRK2s, not only of the ABA insensitive 1 (ABI1) phosphatase, which was identified earlier, but also of another protein phosphatase 2C, PP2CA. The activity of both phosphatases was inhibited by about 50% in the presence of 50 μM PA. PA 16:0/18:1 also impacts the phosphorylation and subcellular localization of SnRK2-interacting calcium sensor, known to inhibit SnRK2 activity in a calcium-dependent manner. Thus, PA was found to regulate ABA-non-activated SnRK2 signaling at several levels: the activity, phosphorylation status and/or localization of SnRK2 cellular partners.

From Survival to Productivity Mode: Cytokinins Allow Avoiding the Avoidance Strategy Under Stress Conditions

Growth retardation and stress-induced premature plant senescence are accompanied by a severe yield reduction and raise a major agro-economic concern. To improve biomass and yield in agricultural crops under mild stress conditions, the survival must be changed to productivity mode. Our previous successful attempts to delay premature senescence and growth inhibition under abiotic stress conditions by autoregulation of cytokinins (CKs) levels constitute a generic technology toward the development of highly productive plants. Since this technology is based on the induction of CKs synthesis during the age-dependent senescence phase by a senescence-specific promoter (SARK), which is not necessarily regulated by abiotic stress conditions, we developed autoregulating transgenic plants expressing the IPT gene specifically under abiotic stress conditions. The Arabidopsis promoter of the stress-induced metallothionein gene (AtMT) was isolated, fused to the IPT gene and transformed into tobacco plants. The MT:IPT transgenic tobacco plants displayed comparable elevated biomass productivity and maintained growth under drought conditions. To decipher the role and the molecular mechanisms of CKs in reverting the survival transcriptional program to a sustainable plant growth program, we performed gene expression analysis of candidate stress-related genes and found unexpectedly clear downregulation in the CK-overproducing plants. We also investigated kinase activity after applying exogenous CKs to tobacco cell suspensions that were grown in salinity stress. In-gel kinase activity analysis demonstrated CK-dependent deactivation of several stress-related kinases including two of the MAPK components, SIPK and WIPK and the NtOSAK, a member of SnRK2 kinase family, a key component of the ABA signaling cascade. A comprehensive phosphoproteomics analysis of tobacco cells, treated with exogenous CKs under salinity-stress conditions indicated that >50% of the identified phosphoproteins involved in stress responses were dephosphorylated by CKs. We hypothesize that upregulation of CK levels under stress conditions desensitize stress signaling cues through deactivation of kinases that are normally activated under stress conditions. CK-dependent desensitization of environmental stimuli is suggested to attenuate various pathways of the avoidance syndrome including the characteristic growth arrest and the premature senescence while allowing normal growth and metabolic maintenance.

Heterologous expression of an Agropyron cristatum SnRK2 protein kinase gene (AcSnRK2.11) increases freezing tolerance in transgenic yeast and tobacco

The sucrose non-fermenting-1 related protein kinase 2 (SnRK2) family plays an important role in the response to abiotic stress. To characterize the function of the SnRK2 gene from Agropyron cristatum in stress protection, we cloned the complete coding sequence of the AcSnRK2.11 gene from A. cristatum and generated AcSnRK2.11-overexpressing tobacco lines. The open reading frame of AcSnRK2.11 was 1083 bp in length and encoded a polypeptide of 360 amino acid residues. The sequence analysis results showed that AcSnRK2.11 contained conserved domains typified in SnRK2 protein kinases. Subcellular localization analysis showed that AcSnRK2.11 was located in the nucleus. AcSnRK2.11 was constitutively expressed in all of the examined tissues, and its transcription was induced by cold, dehydration, and salt stress, but not by abscisic acid treatment. Overexpression of the AcSnRK2.11 gene conferred freezing tolerance in yeast. AcSnRK2.11-overexpressing tobacco lines showed higher tolerance to freezing stress than did wild-type (WT) based on higher survival rates, lower malondialdehyde content and increased relative water content retention, chlorophyll yields, superoxide dismutase activities, reactive oxygen species content, peroxidase levels, and soluble carbohydrates under low-temperature conditions. The transcripts of NtDREB1, NtDREB2, NtERD10A, NtERD10B, NtERD10C, NtERD10D, NtMnSOD, NtCDPK15, and NtMPK9 in AcSnRK2.11-overexpressing tobacco lines were more abundant than in WT plants under low-temperature stress. These results suggest that AcSnRK2.11 may function as a regulatory factor associated with a cold-response pathway and could be used in plant breeding for cold resistance.

Protein lysine methylation contributes to modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress

The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analysed the importance of protein lysine methylation for plants to cope with cadmium. We analysed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in two cadmium-sensitive species, Arabidopsis thaliana and A. lyrata, and in three populations of A. halleri with contrasting cadmium accumulation and tolerance traits. We showed that some proteins are differentially methylated at lysine residues in response to Cd and that a few genes coding KMTs are regulated by cadmium. Also, we showed that 9 out of 23 A. thaliana mutants disrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, and the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that lysine methylation of non-histone proteins is impacted by cadmium and that several methylation events are important for modulating the response of Arabidopsis plants to cadmium stress.

Two SnRK2-Interacting Calcium Sensor Isoforms Negatively Regulate SnRK2 Activity by Different Mechanisms

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements regulating abscisic acid-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) inhibits SnRK2 activity. Use of alternative transcription start sites located within the Arabidopsis (Arabidopsis thaliana) AtSCS gene results in two in-frame transcripts and subsequently two proteins, that differ only by the sequence position of the N terminus. We previously described the longer AtSCS-A, and now describe the shorter AtSCS-B and compare the two isoforms. The two isoforms differ substantially in their expression profiles in plant organs and in response to environmental stresses, in their calcium binding properties, and in their conformational dynamics in the presence and absence of Ca²⁺ Only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but while AtSCS-A requires calcium for inhibition, AtSCS-B does not. Analysis of Arabidopsis plants stably expressing 35S::AtSCS-A-c-myc or 35S::AtSCS-B-c-myc in the scs-1 knockout mutant background revealed that, in planta, both forms are negative regulators of abscisic acid-induced SnRK2 activity and regulate plant resistance against water deficit. Moreover, the data highlight biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.

Evolution of Abscisic Acid Signaling for Stress Responses to Toxic Metals and Metalloids

Toxic heavy metals and metalloids in agricultural ecosystems are crucial factors that limit global crop productivity and food safety. Industrial toxic heavy metals and metalloids such as cadmium, lead, and arsenic have contaminated large areas of arable land in the world and their accumulation in the edible parts of crops is causing serious health risks to humans and animals. Plants have co-evolved with various concentrations of these toxic metals and metalloids in soil and water. Some green plant species have significant innovations in key genes for the adaptation of abiotic stress tolerance pathways that are able to tolerate heavy metals and metalloids. Increasing evidence has demonstrated that phytohormone abscisic acid (ABA) plays a vital role in the alleviation of heavy metal and metalloid stresses in plants. Here, we trace the evolutionary origins of the key gene families connecting ABA signaling with tolerance to heavy metals and metalloids in green plants. We also summarize the molecular and physiological aspects of ABA in the uptake, root-to-shoot translocation, chelation, sequestration, reutilization, and accumulation of key heavy metals and metalloids in plants. The molecular evolution and interaction between the ABA signaling pathway and mechanisms for heavy metal and metalloid tolerance are highlighted in this review. Therefore, we propose that it is promising to manipulate ABA signaling in plant tissues to reduce the uptake and accumulation of toxic heavy metals and metalloids in crops through the application of ABA-producing bacteria or ABA analogues. This may lead to improvements in tolerance of major crops to heavy metals and metalloids.

Low endogenous NO levels in roots and antioxidant systems are determinants for the resistance of Arabidopsis seedlings grown in Cd

Cadmium (Cd), which is a toxic non-essential heavy metal capable of entering plants and thus the food chain, constitutes a major environmental and health concern worldwide. An understanding of the tools used by plants to overcome Cd stress could lead to the production of food crops with lower Cd uptake capacity and of plants with greater Cd uptake potential for phytoremediation purposes in order to restore soil efficiency in self-sustaining ecosystems. The signalling molecule nitric oxide (NO), whose function remains unclear, has recently been involved in responses to Cd stress. Using different mutants, such as nia1nia2, nox1, argh1-1 and Atnoa1, which were altered in NO metabolism, we analysed various parameters related to reactive oxygen and nitrogen species (ROS/RNS) metabolism and seedling fitness following germination and growth under Cd treatment conditions for seven days. Seedling roots were the most affected, with an increase in ROS and RNS observed in wild type (WT) seedling roots, leading to increased oxidative damage and fitness loss. Mutants that showed lower NO levels in seedling roots under Cd stress were more resistant than WT seedlings due to the maintenance of antioxidant systems which protect against oxidative damage.

Reactive oxygen species, auxin and nitric oxide in metal-stressed roots: toxicity or defence

The presented review is a summary on the current knowledge about metal induced stress response in plants, focusing on the roles of reactive oxygen species, auxin and nitric oxide in roots. The article focuses mainly on the difference between defence and toxicity symptoms of roots during metal-induced stress. Nowadays, pollution of soils by heavy metals is a rapidly growing issue, which affects agriculture and human health. In order to deal with these problems, we must first understand the basic mechanisms and responses to environmental conditions in plants growing under such conditions. Studies so far show somewhat conflicting data, interpreting the same stress responses as both symptoms of defence and toxicity. Therefore, the aim of this review is to give a report about current knowledge of heavy metal-induced stress research, and also to differentiate between toxicity and defence, and outline the challenges of research, focusing on reactive oxygen and nitrogen species, auxin, and the interplay among them. There are still remaining questions on how reactive oxygen and nitrogen species, as well as auxin, can activate either symptoms of toxicity or defence, and adaptation responses.

Enhanced nitric oxide generation mitigates cadmium toxicity via superoxide scavenging leading to the formation of peroxynitrite in barley root tip

The aim of this study was to observe the possible function of increased superoxide and NO production in the response of barley root tip to the harmful level of Cd. While superoxide generation was detected only in the transition zone, the formation of NO was observed in the apical elongation zones of the control root tips. However, the root region with the superoxide generation was also associated with peroxynitrite specific fluorescence signal. Superoxide, H₂O₂ and peroxynitrite generation increased with Cd treatment in a dose-dependent manner. In turn, NO level increased at low 10-20 μM but decreased at high 50-60 μM Cd concentrations in comparison with the control. While co-treatment of roots with rotenone markedly attenuated the Cd-induced superoxide generation and lipid peroxidation, it increased the level of NO in the root tips. Although rotenone did not influence the Cd-induced increase of GPX activity at 10-30 μM Cd concentrations, it markedly reversed the high 40-60 μM Cd concentrations-induced decline of GPX activity. Cd-induced cell death was associated with robust superoxide generation, but not with a high level of peroxynitrite. The Cd-evoked inhibition of root growth was significantly reversed by a strong antioxidant N-acetyl cysteine but not by a peroxynitrite scavenger uric acid, suggesting that similarly to Cd-induced cell death, an imbalance in the ROS homeostasis and not an enhanced level of peroxynitrite is responsible for the Cd-induced root growth inhibition. Based on these findings, it can be assumed that NO acts mainly in the regulation of superoxide level in the tips of root. Under Cd stress, the enhanced NO level is involved in the scavenging of highly toxic superoxide through the formation of peroxynitrite, thus reducing the superoxide-mediated cell death in barley root.

Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress

Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20–22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs.

The polish wheat (Triticum polonicum L.) TpSnRK2.10 and TpSnRK2.11 meditate the accumulation and the distribution of cd and Fe in transgenic Arabidopsis plants

Background

The SnRK2s (Plant specific protein kinase) are involved in various biological processes, such as plant defense and environmental challenges. In Arabidopsis, AtSnRK2s regulate the expression of some metal transporters. For example, AtSnRK2.4 plays a role in the regulation of Arabidopsis tolerance to Cd; AtSnRK2.2 and AtSnRK2.3 are involved in Cd uptake and translocation. However, the functions of their homologs, TpSnRK2.10 and TpSnRK2.11 from dwarf Polish wheat are unknown.

Results

TpSnRK2.11 encodes a cytoplasmic protein. TpSnRK2.10 and TpSnRK2.11 have different expression patterns at different growth stages. Expression of TpSnRK2.10 increased yeast’s sensitivity to Cd; conversely, expression of TpSnRK2.11 enhanced yeast’s tolerance to Cd. Overexpression of TpSnRK2.10 or TpSnRK2.11 did not affect Cd sensitivity in Arabidopsis, but significantly increased Cd accumulation in roots and shoots, and Cd translocation from roots to shoots. While, Fe accumulation was significantly increased in roots but decreased in shoots by overexpression of TpSnRK2.10; opposite results were observed in TpSnRK2.11-overexpressing lines. Subcellular distribution analysis found that overexpression of TpSnRK2.10 and TpSnRK2.11 increased Cd concentration in cell wall and organelle fractions of roots and shoots; meanwhile, they also differentially influenced Fe distribution.

Conclusions

These results indicated that TpSnRK2.10 and TpSnRK2.11 are involved in the uptakes and the translocations of Cd and Fe, possibly by regulating the expression of AtNRAMP1 and AtHMA4, and other genes involved in the synthesis of phytochelatins or hemicellolosic polysaccharides.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5589-1) contains supplementary material, which is available to authorized users.

Phosphoproteomic analysis reveals that dehydrins ERD10 and ERD14 are phosphorylated by SNF1-related protein kinase 2.10 in response to osmotic stress

SNF1-related protein kinases 2 (SnRK2s) regulate the plant responses to abiotic stresses, especially water deficits. They are activated in plants subjected to osmotic stress, and some of them are additionally activated in response to enhanced concentrations of abscisic acid (ABA) in plant cells. The SnRK2s that are activated in response to ABA are key elements of ABA signalling that regulate plant acclimation to environmental stresses and ABA-dependent development. Much less is known about the SnRK2s that are not activated by ABA, albeit several studies have shown that these kinases are also involved in response to osmotic stress. Here, we show that one of the Arabidopsis thaliana ABA-non-activated SnRK2s, SnRK2.10, regulates not only the response to salinity but also the plant sensitivity to dehydration. Several potential SnRK2.10 targets phosphorylated in response to stress were identified by a phosphoproteomic approach, including the dehydrins ERD10 and ERD14. Their phosphorylation by SnRK2.10 was confirmed in vitro. Our data suggest that the phosphorylation of ERD14 within the S-segment is involved in the regulation of dehydrin subcellular localization in response to stress.

Thermodynamic insights into an interaction between ACYL-CoA-BINDING PROTEIN2 and LYSOPHOSPHOLIPASE2 in Arabidopsis

Lysophospholipids (LPLs) are important lipid-signaling molecules in plants, of which lysophosphatidylcholine (lysoPC) is one of the most well-characterized LPLs, having important roles in plant stress responses. It is broken down by lysophospholipases, but the molecular mechanism involved in lysoPC degradation is unclear. Recombinant Arabidopsis thaliana ACYL-CoA-BINDING PROTEIN2 (AtACBP2) has been reported to bind lysoPC via its acyl-CoA-binding domain and also LYSOPHOSPHOLIPASE 2 (AtLYSOPL2) via its ankyrin repeats in vitro To investigate the interactions of AtACBP2 with AtLYSOPL2 and lysoPC in more detail, we conducted isothermal titration calorimetry with AtACBP2_70-354, an AtACBP2 derivative consisting of amino acids 70-354, containing both the acyl-CoA-binding domain and ankyrin repeats. We observed that the interactions of AtACBP2_70-354 with AtLYSOPL2 and lysoPC were both endothermic, favored by solvation entropy and opposed by enthalpy, with dissociation constants in the micromolar range. Of note, three AtLYSOPL2 catalytic triad mutant proteins (S147A, D268A, and H298A) bound lysoPC only weakly, with an exothermic burst and dissociation constants in the millimolar range. Furthermore, the binding affinity of lysoPC-premixed AtACBP2_70-354 to AtLYSOPL2 was 10-fold higher than that of AtACBP2_70-354 alone to AtLYSOPL2. We conclude that AtACBP2 may play a role in facilitating a direct interaction between AtLYSOPL2 and lysoPC. Our results suggest that AtACBP2_70-354 probably binds to lysoPC through a hydrophobic interface that enhances a hydrotropic interaction of AtACBP2_70-354 with AtLYSOPL2 and thereby facilitates AtLYSOPL2's lysophospholipase function.

SNF1-Related Protein Kinases SnRK2.4 and SnRK2.10 Modulate ROS Homeostasis in Plant Response to Salt Stress

In response to salinity and various other environmental stresses, plants accumulate reactive oxygen species (ROS). The ROS produced at very early stages of the stress response act as signaling molecules activating defense mechanisms, whereas those produced at later stages in an uncontrolled way are detrimental to plant cells by damaging lipids, DNA, and proteins. Multiple systems are involved in ROS generation and also in ROS scavenging. Their level and activity are tightly controlled to ensure ROS homeostasis and protect the plant against the negative effects of the environment. The signaling pathways responsible for maintaining ROS homeostasis in abiotic stress conditions remain largely unknown. Here, we show that in Arabidopsis thaliana, two abscisic acid- (ABA)-non-activated SNF1-releted protein kinases 2 (SnRK2) kinases, SnRK2.4 and SnRK2.10, are involved in the regulation of ROS homeostasis in response to salinity. They regulate the expression of several genes responsible for ROS generation at early stages of the stress response as well as those responsible for their removal. Moreover, the SnRK2.4 regulate catalase levels and its activity and the level of ascorbate in seedlings exposed to salt stress.

Expression of the Tobacco Non-symbiotic Class 1 Hemoglobin Gene Hb1 Reduces Cadmium Levels by Modulating Cd Transporter Expression Through Decreasing Nitric Oxide and ROS Level in Arabidopsis

Hemoglobin (Hb) proteins are ubiquitous in plants, and non-symbiotic class 1 hemoglobin (Hb1) is involved in various biotic and abiotic stress responses. Here, the expression of the tobacco (Nicotiana tabacum) hemoglobin gene NtHb1 in Arabidopsis (Arabidopsis thaliana) showed higher cadmium (Cd) tolerance and lower accumulations of Cd, nitric oxide (NO), and reactive oxygen species (ROS) like hydrogen peroxide (H₂O₂). NtHb1-expressing Arabidopsis exhibited a reduced induction of NO levels in response to Cd, suggesting scavenging of NO by Hb1. In addition, transgenic plants had reduced accumulation of ROS and increased activities of antioxidative enzymes (catalase, superoxide dismutase, and glutathione reductase) in response to Cd. While the expression of the Cd exporters ABC transporter (PDR8) and Ca²⁺/H⁺ exchangers (CAXs) was increased, that of the Cd importers iron responsive transporter 1 (IRT1) and P-type 2B Ca²⁺ ATPase (ACA10) was reduced in response to Cd. When Col-0 plants were treated with the NO donor sodium nitroprusside (SNP) and H₂O₂, the expression pattern of Cd transporters (PDR8, CAX3, IRT1, and ACA10) was reversed, suggesting that NtHb1 expression decreased the Cd level by regulating the expression of Cd transporters via decreased NO and ROS. Correspondingly, NtHb1-expressing Arabidopsis showed increased Cd export. In summary, the expression of NtHb1 reduces Cd levels by regulating Cd transporter expression via decreased NO and ROS levels in Arabidopsis.

Vacuolar Transporters for Cadmium and Arsenic in Plants and their Applications in Phytoremediation and Crop Development

Soil contamination by heavy metals and metalloids such as cadmium (Cd) and arsenic (As) poses a major threat to the environment and to human health. Vacuolar sequestration is one of the main mechanisms by which plants control toxic materials including Cd and As. Understanding the mechanisms of heavy metal tolerance and accumulation can be useful for both phytoremediation and safe crop development. In this review, we summarize recent advances in deciphering the molecular mechanisms underlying vacuolar sequestration of Cd and As, and discuss potential biotechnological applications of this knowledge and efforts towards attaining these goals.

The phosphatidic acid paradox: Too many actions for one molecule class? Lessons from plants

Phosphatidic acid (PA) is a simple phospholipid observed in most organisms. PA acts as a key metabolic intermediate and a second messenger that regulates many cell activities. In plants, PA is involved in numerous cell responses induced by hormones, stress inputs and developmental processes. Interestingly, PA production can be triggered by opposite stressors, such as cold and heat, or by hormones that are considered to be antagonistic, such as abscisic acid and salicylic acid. This property questions the specificity of the responses controlled by PA. Are there generic responses to PA, meaning that cell regulation triggered by PA would be always the same, even in opposite physiological situations? Alternatively, do the responses to PA differ according to the physiological context within the cells? If so, the mechanisms that regulate the divergence of PA-controlled reactions are poorly defined. This review summarizes the latest opinions on how PA signalling is directed in plant cells and examines the intrinsic properties of PA that enable its regulatory diversity. We propose a concept whereby PA regulatory messages are perceived as complex "signatures" that take into account their production site, the availability of target proteins and the relevant cellular environments.

Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

BACKGROUND

The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale.

RESULTS

We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment. A multiplicity of the identified 1772 DEGs were implicated in hormone signaling and transcriptional regulation, particularly NACs and WRKYs were all upregulated under Cd stress. All of the 6 Cd-upregulated ABC transporters were pleiotropic drug resistance proteins (PDRs), whereas all of the 6 ZRT/IRT-like proteins (ZIPs) were consistently downregulated by Cd treatment. To further confirm our results of this early transcriptomic response to Cd exposure, we then conducted weighted gene co-expression network analysis (WGCNA) to re-analyze our RNAseq data in combination with other 11 previously published RNAseq datasets for rice roots exposed to diverse concentrations of Cd for extended treatment periods. This integrative approach identified 271 transcripts as universal Cd-regulated DEGs that are key components of the Cd treatment coupled co-expression module. A global view of the 164 transcripts with annotated functions in pathway networks revealed several Cd-upregulated key functional genes, including transporter ABCG36/OsPDR9, 12-oxo-phytodienoic acid reductases (OPRs) for JA synthesis, and ZIM domain proteins JAZs in JA signaling, as well as OsWRKY10, NAC, and ZFP transcription factors. More importantly, 104 of these, including ABCG36/OsPDR9, OsNAC3, as well as several orthologs in group metalloendoproteinase, plastocyanin-like domain containing proteins and pectin methylesterase inhibitor, may respond specifically to various Cd pressures, after subtracting the 60 general stress-responsive genes reported to be commonly upregulated following multiple stresses.

CONCLUSION

An integrative approach was implemented to identify DEGs and co-expression network modules in response to various Cd pressures, and 104 of the 164 annotatable universal Cd-responsive DEGs may specifically respond to various Cd pressures. These results provide insight into the universal molecular mechanisms beneath the Cd response in rice roots, and suggest many promising targets for improving the rice acclimation process against Cd toxicity.

Redox regulation of a guard cell SNF1-related protein kinase in Brassica napus, an oilseed crop

Kinase-mediated phosphorylation is a pivotal regulatory process in stomatal responses to stresses. Through a redox proteomics study, a sucrose non-fermenting 1-related protein kinase (SnRK2.4) was identified to be redox-regulated in Brassica napus guard cells upon abscisic acid treatment. There are six genes encoding SnRK2.4 paralogs in B. napus Here, we show that recombinant BnSnRK2.4-1C exhibited autophosphorylation activity and preferentially phosphorylated the N-terminal region of B. napus slow anion channel (BnSLAC1-NT) over generic substrates. The in vitro activity of BnSnRK2.4-1C requires the presence of manganese (Mn²⁺). Phosphorylation sites of autophosphorylated BnSnRK2.4-1C were mapped, including serine and threonine residues in the activation loop. In vitro BnSnRK2.4-1C autophosphorylation activity was inhibited by oxidants such as H₂O₂ and recovered by active thioredoxin isoforms, indicating redox regulation of BnSnRK2.4-1C. Thiol-specific isotope tagging followed by mass spectrometry analysis revealed specific cysteine residues responsive to oxidant treatments. The in vivo activity of BnSnRK2.4-1C is inhibited by 15 min of H₂O₂ treatment. Taken together, these data indicate that BnSnRK2.4-1C, an SnRK preferentially expressed in guard cells, is redox-regulated with potential roles in guard cell signal transduction.

De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome

Gene regulation at the transcriptional and translational level leads to diversity in phenotypes and function in organisms. Regulatory DNA or RNA sequence motifs adjacent to the gene coding sequence act as binding sites for proteins that in turn enable or disable expression of the gene. Whereas the known DNA and RNA binding proteins range in the thousands, only a few motifs have been examined. In this study, we have predicted putative regulatory motifs in groups of untranslated regions from genes regulated at the translational level in Arabidopsis thaliana under normal and stressed conditions. The test group of sequences was divided into random subgroups and subjected to three de novo motif finding algorithms (Seeder, Weeder and MEME). In addition to identifying sequence motifs, using an in silico tool we have predicted microRNA target sites in the 3′ UTRs of the translationally regulated genes, as well as identified upstream open reading frames located in the 5′ UTRs. Our bioinformatics strategy and the knowledge generated contribute to understanding gene regulation during stress, and can be applied to disease and stress resistant plant development.

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

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

The role of ZmWRKY4 in regulating maize antioxidant defense under cadmium stress

WRKY transcription factors act as positive regulators in abiotic stress responses by activation of the cellular antioxidant systems. However, there are few reports on the response of WRKY genes to cadmium (Cd) stress. In this study, the role of maize ZmWRKY4 in regulating antioxidant enzymes in Cd stress was investigated. The results indicated that Cd induced up-regulation of the expression and the activities of ZmWRKY4 and superoxide dismutase (SOD) and ascorbate peroxidase (APX). Transient expression and RNA interference (RNAi) silencing of ZmWRKY4 in maize mesophyll protoplasts further revealed that ZmWRKY4 was required for the abscisic acid (ABA)-induced increase in expression and activity of SOD and APX. Overexpression of ZmWRKY4 in protoplasts upregulated the expression and the activities of antioxidant enzymes, whereas ABA induced increases in the expression and the activities of antioxidant enzymes were blocked by the RNAi silencing of ZmWRKY4. Bioinformatic analysis indicated that ZmSOD4 and ZmcAPX both harbored two W-boxes, binding motif for WRKY transcription factors, in their promoter region. Intriguingly, ZmWRKY4 belongs to group I WRKYs with two WRKY domains. Moreover, the synchronized expression patterns indicate that ZmWRKY4 might play a critical role in either regulating the ZmSOD4 and ZmcAPX expression or cooperating with them in response to stress and phytohormone.

A role for CK2 β subunit 4 in the regulation of plant growth, cadmium accumulation and H2O2 content under cadmium stress in Arabidopsis thaliana

Protein kinase CK2, which consists of two α and two β subunits, plays an essential role in plant development and is implicated in plant responses to abiotic stresses, including salt and heat. However, the function of CK2 in response to heavy metals such as cadmium (Cd) has not yet been established. In this study, the transgenic line CKB4ox, which overexpresses CKB4 encoding the CK2β subunit and has elevated CK2 activity, was used to investigate the potential role of CK2 in response to Cd stress in Arabidopsis thaliana. Under Cd stress, CKB4ox showed reduced root growth and biomass accumulation as well as decreased chlorophyll and proline contents compared with wild type. Furthermore, increased Cd accumulation and a higher H₂O₂ content were found in CKB4ox, possibly contributing to the inhibition of CKB4ox growth under Cd stress. Additionally, altered levels of Cd and H₂O₂ were found to be associated with decreased expression of genes involved in Cd efflux, Cd sequestration and H₂O₂ scavenging. Taken together, these results suggest that elevated expression of CKB4 and increased CK2 activity enhance the sensitivity of plants to Cd stress by affecting Cd and H₂O₂ accumulation, including the modulation of genes involved in Cd transport and H₂O₂ scavenging. This study provides direct evidence for the involvement of plant CK2 in the response to Cd stress.

Comparative transcriptome profiling of two Brassica napus cultivars under chromium toxicity and its alleviation by reduced glutathione

BACKGROUND

Chromium (Cr) being multifarious industrial used element, is considered a potential environmental threat. Cr found to be a prospective water and soil pollutant, and thus it is a current area of concern. Oilseed rape (Brassica napus L.) is well known as a major source of edible oil around the globe. Due to its higher growth, larger biomass and capability to uptake toxic materials B. napus is considered a potential candidate plant against unfavorable conditions. To date, no study has been done that described the Cr and GSH mechanism at RNA-Seq level.

RESULTS

Both digital gene expression (DGE) and transcriptome profile analysis (TPA) approaches had opened new insights to uncover the several number of genes related to Cr stress and GSH alleviating mechanism in two leading cultivars (ZS 758 and Zheda 622) of B. napus plants. Data showed that Cr inhibited KEGG pathways i.e. stilbenoid, diarlyheptanoid and gingerol biosynthesis; limonene and pentose degradation and glutathione metabolism in ZS 758; and ribosome and glucosinolate biosynthesis in Zheda-622. On the other hand, vitamin B6, tryptophan, sulfur, nitrogen and fructose and manose metabolisms were induced in ZS 758, and zeatin biosynthesis, linoleic acid metabolism, arginine and proline metabolism, and alanine, asparate and glutamate metabolism pathways in Zheda 622. Cr increased the TFs that were related to hydralase activity, antioxidant activity, catalytic activity phosphatase and pyrophosphatase activity in ZS 758, and vitamin binding and oxidoreductase activity in Zheda 622. Cr also up-regulated the promising proteins related to intracellular membrane bounded organelles, nitrile hyrdatase activity, cytoskeleton protein binding and stress response. It also uncovered, a novel Cr-responsive protein (CL2535.Contig1_All) that was statistically increased as compared to control and GSH treated plants. Exogenously applied GSH successfully not only recovered the changes in metabolic pathways but also induced cysteine and methionine metabolism in ZS 758 and ubiquinone and other terpenoid-quinone biosynthesis pathways in Zheda 622. Furthermore, GSH increased the level of TFs i.e. the gene expression of antioxidant and catalytic activities, iron ion binding and hydrolase activity as compared with Cr. Moreover, results pointed out a novel GSH responsive protein (CL827.Contig3_All) whose expression was found to be significantly increased when compared than Cr stress. Results further delineated that GSH induced TFs such as glutathione disulphide oxidoreducatse and aminoacyl-tRNA ligase activity, and beta glucosidase activity in ZS 758. Similarly in Zheda 622, GSH induced the TFs for instance DNA binding and protein dimerization activity. GSH also highlighted the proteins that were involved in transportation, photosynthesis process, RNA polymerase activity, and against the metal toxicity. These results indicated that cultivar ZS 758 had better metabolism and showed higher tolerance against Cr toxicity.

CONCLUSION

The responses of ZS 758 and Zheda 622 differed considerably at both physiological and transcriptional level. Moreover, RNA-Seq method explored the hazardous behavior of Cr as well as GSH up-regulating mechanism by activating plant metabolism, stress responsive genes, TFs and protein encyclopedia.

Phosphatase ABI1 and okadaic acid-sensitive phosphoprotein phosphatases inhibit salt stress-activated SnRK2.4 kinase

BACKGROUND

SNF1-related protein kinases 2 (SnRK2s) are key regulators of the plant response to osmotic stress. They are transiently activated in response to drought and salinity. Based on a phylogenetic analysis SnRK2s are divided into three groups. The classification correlates with their response to abscisic acid (ABA); group 1 consists SnRK2s non-activated in response to ABA, group 2, kinases non-activated or weakly activated (depending on the plant species) by ABA treatment, and group 3, ABA-activated kinases. The activity of all SnRK2s is regulated by phosphorylation. It is well established that clade A phosphoprotein phosphatases 2C (PP2Cs) are negative regulators of ABA-activated SnRK2s, whereas regulators of SnRK2s from group 1 remain unidentified.

RESULTS

Here, we show that ABI1, a PP2C clade A phosphatase, interacts with SnRK2.4, member of group 1 of the SnRK2 family, dephosphorylates Ser158, whose phosphorylation is needed for the kinase activity, and inhibits the kinase, both in vitro and in vivo. Our data indicate that ABI1 and the kinase regulate primary root growth in response to salinity; the phenotype of ABI1 knockout mutant (abi1td) exposed to salt stress is opposite to that of the snrk2.4 mutant. Moreover, we show that the activity of SnRK2s from group 1 is additionally regulated by okadaic acid-sensitive phosphatase(s) from the phosphoprotein phosphatase (PPP) family.

CONCLUSIONS

Phosphatase ABI1 and okadaic acid-sensitive phosphatases of the PPP family are negative regulators of salt stress-activated SnRK2.4. The results show that ABI1 inhibits not only the ABA-activated SnRK2s but also at least one ABA-non-activated SnRK2, suggesting that the phosphatase is involved in the cross talk between ABA-dependent and ABA-independent stress signaling pathways in plants.

Physiological and proteomics analyses reveal the mechanism of Eichhornia crassipes tolerance to high-concentration cadmium stress compared with Pistia stratiotes

Cadmium (Cd) pollution is an environmental problem worldwide. Phytoremediation is a convenient method of removing Cd from both soil and water, but its efficiency is still low, especially in aquatic environments. Scientists have been trying to improve the ability of plants to absorb and accumulate Cd based on interactions between plants and Cd, especially the mechanism by which plants resist Cd. Eichhornia crassipes and Pistia stratiotes are aquatic plants commonly used in the phytoremediation of heavy metals. In the present study, we conducted physiological and biochemical analyses to compare the resistance of these two species to Cd stress at 100 mg/L. E. crassipes showed stronger resistance and was therefore used for subsequent comparative proteomics to explore the potential mechanism of E. crassipes tolerance to Cd stress at the protein level. The expression patterns of proteins in different functional categories revealed that the physiological activities and metabolic processes of E. crassipes were affected by exposure to Cd stress. However, when some proteins related to these processes were negatively inhibited, some analogous proteins were induced to compensate for the corresponding functions. As a result, E. crassipes could maintain more stable physiological parameters than P. stratiotes. Many stress-resistance substances and proteins, such as proline and heat shock proteins (HSPs) and post translational modifications, were found to be involved in the protection and repair of functional proteins. In addition, antioxidant enzymes played important roles in ROS detoxification. These findings will facilitate further understanding of the potential mechanism of plant response to Cd stress at the protein level.

NO signaling in plant immunity: a tale of messengers

Nitric oxide (NO) is a free radical gas involved in a myriad of plant physiological processes including immune responses. How NO mediates its biological effects in plant facing microbial pathogen attack is an unresolved question. Insights into the molecular mechanisms by which it propagates signals reveal the contribution of this simple gas in complex signaling pathways shared with reactive oxygen species (ROS) and the second messenger Ca(2+). Understanding of the subtle cross-talks operating between these signals was greatly improved by the recent identification and the functional analysis of proteins regulated through S-nitrosylation, a major NO-dependent post-translational protein modification. Overall, these findings suggest that NO is probably an important component of the mechanism coordinating and regulating Ca(2+) and ROS signaling in plant immunity.

Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in Senescing Barley leaves

Leaf senescence is a tightly regulated developmental or stress-induced process. It is accompanied by dramatic changes in cell metabolism and structure, eventually leading to the disintegration of chloroplasts, the breakdown of leaf proteins, internucleosomal fragmentation of nuclear DNA and ultimately cell death. In light of the global and intense reorganization of the senescing leaf transcriptome, measuring time-course gene expression patterns in this model is challenging due to the evident problems associated with selecting stable reference genes. We have used oligonucleotide microarray data to identify 181 genes with stable expression in the course of dark-induced senescence of barley leaf. From those genes, we selected 5 candidates and confirmed their invariant expression by both reverse transcription quantitative PCR and droplet digital PCR (ddPCR). We used the selected reference genes to normalize the level of the expression of the following senescence-responsive genes in ddPCR assays: SAG12, ICL, AGXT, CS and RbcS. We were thereby able to achieve a substantial reduction in the data variability. Although the use of reference genes is not considered mandatory in ddPCR assays, our results show that it is advisable in special cases, specifically those that involve the following conditions: i) a low number of repeats, ii) the detection of low-fold changes in gene expression or iii) series data comparisons (such as time-course experiments) in which large sample variation greatly affects the overall gene expression profile and biological interpretation of the data.

Interplays between nitric oxide and reactive oxygen species in cryptogein signalling

Nitric oxide (NO) has many functions in plants. Here, we investigated its interplays with reactive oxygen species (ROS) in the defence responses triggered by the elicitin cryptogein. The production of NO induced by cryptogein in tobacco cells was partly regulated through a ROS-dependent pathway involving the NADPH oxidase NtRBOHD. In turn, NO down-regulated the level of H2O2. Both NO and ROS synthesis appeared to be under the control of type-2 histone deacetylases acting as negative regulators of cell death. Occurrence of an interplay between NO and ROS was further supported by the finding that cryptogein triggered a production of peroxynitrite (ONOO(-)). Next, we showed that ROS, but not NO, negatively regulate the intensity of activity of the cryptogein-induced protein kinase NtOSAK. Furthermore, using a DNA microarray approach, we identified 15 genes early induced by cryptogein via NO. A part of these genes was also modulated by ROS and encoded proteins showing sequence identity to ubiquitin ligases. Their expression appeared to be negatively regulated by ONOO(-), suggesting that ONOO(-) mitigates the effects of NO and ROS. Finally, we provided evidence that NO required NtRBOHD activity for inducing cell death, thus confirming previous assumption that ROS channel NO through cell death pathways.

Dark-induced senescence of barley leaves involves activation of plastid transglutaminases

Transglutaminases (E.C. 2.3.2.13) catalyze the post-translational modification of proteins by establishing ε-(γ-glutamyl) lysine isopeptide bonds and by the covalent conjugation of polyamines to endo-glutamyl residues of proteins. In light of the confirmed role of transglutaminases in animal cell apoptosis and only limited information on the role of these enzymes in plant senescence, we decided to investigate the activity of chloroplast transglutaminases (ChlTGases) and the fate of chloroplast-associated polyamines in Hordeum vulgare L. 'Nagrad' leaves, where the senescence process was induced by darkness (day 0) and continued until chloroplast degradation (day 12). Using an anti-TGase antibody, we detected on a subcellular level, the ChlTGases that were associated with destacked/degraded thylakoid membranes, and beginning on day 5, were also found in the stroma. Colorimetric and radiometric assays revealed during senescence an increase in ChlTGases enzymatic activity. The MS/MS identification of plastid proteins conjugated with exogenous polyamines had shown that the ChlTGases are engaged in the post-translational modification of proteins involved in photosystem organization, stress response, and oxidation processes. We also computationally identified the cDNA of Hv-Png1-like, a barley homologue of the Arabidopsis AtPng1 gene. Its mRNA level was raised from days 3 to 10, indicating that transcriptional regulation controls the activity of barley ChlTGases. Together, the presented results deepen our knowledge of the mechanisms of the events happened in dark-induced senescence of barley leaves that might be activation of plastid transglutaminases.

The plant kinome

Plant kinases are one of the largest protein families in Arabidopsis. There are almost 600 membrane-located receptor kinases and almost 400 soluble kinases with distinct functions in signal transduction. In this minireview we discuss phylogeny and functional context of prominent members from major protein kinase subfamilies in plants.

Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation

Background

Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been historically consumed by local populations in the desert regions of northwest China. Sand rice is a potential food crop resilient to ongoing climate change; however, partly due to the scarcity of genetic information, this species has undergone only little agronomic modifications through classical breeding during recent years.

Results

We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741 unigenes. Phylogenetic analysis based on 221 single-copy genes showed close relationship between sand rice and the recently domesticated crop sugar beet. Transcriptomic comparisons also showed a high level of global sequence conservation between these two species. Conservation of sand rice and sugar beet orthologs assigned to response to salt stress gene ontology term suggests that sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far more tolerant to high temperature. A set of genes likely relevant for resistance to heat stress, was functionally annotated according to expression levels, sequence annotation, and comparisons corresponding transcriptome profiling results in Arabidopsis.

Conclusions

The present work provides abundant genomic information for functional dissection of the important traits in sand rice. Future screening the genetic variation among different ecotypes and constructing a draft genome sequence will further facilitate agronomic trait improvement and final domestication of sand rice.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-872) contains supplementary material, which is available to authorized users.

Cadmium-induced cell death in BY-2 cell culture starts with vacuolization of cytoplasm and terminates with necrosis

Cadmium is a potent inducer of programmed cell death (PCD) in plants but the morphological changes in cells exposed to cadmium are poorly characterized. Using light and transmission electron microscopy (TEM) we have investigated the changes in ultrastructure of tobacco BY-2 cells treated with 50 µM CdSO4. The cadmium-induced alterations in cell morphology occurred gradually over a period of 3-4 days and the first stages of the response resembled vacuolar type of cell death. The initial formation of numerous small cytoplasmic vacuoles and dilation of endoplasmic reticulum was followed first by fusion of smaller vacuoles with each other and with big vacuoles, and then by the appearance of autophagic vacuoles containing autophagic bodies. The final stages of cell death were accompanied by necrotic features including loss of plasmalemma integrity, shrinkage of the protoplast and unprocessed cellular components. In addition, we observed a gradual degradation of nuclear material. Our results demonstrate that cadmium-induced plant cell death is a slow process featuring elements of vacuolar cell death and terminating with necrosis.