Overexpression of sugarcane gene SoSnRK2.1 confers drought tolerance in transgenic tobacco

H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane

Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress.

Silencing the CsSnRK2.11 Gene Decreases Drought Tolerance of Cucumis sativus L

Drought stress restricts vegetable growth, and abscisic acid plays an important role in its regulation. Sucrose non-fermenting1-related protein kinase 2 (SnRK2) is a key enzyme in regulating ABA signal transduction in plants, and it plays a significant role in response to multiple abiotic stresses. Our previous experiments demonstrated that the SnRK2.11 gene exhibits a significant response to drought stress in cucumbers. To further investigate the function of SnRK2.11 under drought stress, we used VIGS (virus-induced gene silencing) technology to silence this gene and conducted RNA-seq analysis. The SnRK2.11-silencing plants displayed increased sensitivity to drought stress, which led to stunted growth and increased wilting speed. Moreover, various physiological parameters related to photosynthesis, chlorophyll fluorescence, leaf water content, chlorophyll content, and antioxidant enzyme activity were significantly reduced. The intercellular CO2 concentration, non-photochemical burst coefficient, and malondialdehyde and proline content were significantly increased. RNA-seq analysis identified 534 differentially expressed genes (DEGs): 311 were upregulated and 223 were downregulated. GO functional annotation analysis indicated that these DEGs were significantly enriched for molecular functions related to host cells, enzyme activity, and stress responses. KEGG pathway enrichment analysis further revealed that these DEGs were significantly enriched in phytohormone signalling, MAPK signalling, and carotenoid biosynthesis pathways, all of which were associated with abscisic acid. This study used VIGS technology and transcriptome data to investigate the role of CsSnRK2.11 under drought stress, offering valuable insights into the mechanism of the SnRK2 gene in enhancing drought resistance in cucumbers.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis

BACKGROUND

Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family.

RESULT

We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation.

CONCLUSION

This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses.

xCO2 temporal variability above Brazilian agroecosystems: A remote sensing approach

Agriculture and soil management practices are closely related to CO₂ emissions in crop fields. These practices directly interfere on the carbon dynamics between the land and atmosphere. In this study, we investigated the temporal variability of the column-averaged dry-air mole fraction of atmospheric CO₂ (xCO₂), solar-induced chlorophyll fluorescence (SIF), and the normalized difference vegetation index (NDVI) in areas with the main agroecosystems in southern-central Brazil as a way to understand if and how crops cycle and agricultural management could be associated with the temporal variability of NDVI, SIF and xCO₂. The study was carried out in areas corresponding to the three agroecosystems': sugarcane (Pradópolis, State of São Paulo, Brazil), cropland with soybean-corn succession (Santo Antônio do Paraíso, State of Paraná, Brazil), and grassland (Águas Claras, State of Mato Grosso do Sul, Brazil). Air temperature, precipitation, NDVI, and SIF and xCO₂ were retrieved from NASA-POWER, NASA-GIOVANNI, SATVeg-EMBRAPA, and OCO-2, respectively, during a two-year study. Trends were removed from the NDVI, SIF, and xCO₂ time series applying the regression method. A negative correlation between SIF and xCO₂ was found in sugarcane and cropland areas, but in grasslands, no correlation showed up. Higher SIF values were observed in grassland (2.24 W m-2 sr-1 μm-1), and lower xCO₂ values were observed above grains, which varied from 396.8 to 404.2 ppm. Both xCO₂ and SIF followed more a seasonal pattern in sugarcane and annual crops, but over pasture this presented an unusual pattern related to higher precipitation events. Our results indicate a potential use of SIF and xCO₂ which could help identifying potential sources and sinks of the main additional greenhouse gas over agricultural areas.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae)

Sucrose non-fermenting1-related protein kinases (SnRKs) are a type of Ser/Thr protein kinases, and they play an important role in plant life, especially in metabolism and responses to environmental stresses. However, there is limited information on SnRK genes in Dendrobium officinale. In the present research, a total of 36 DoSnRK genes were identified based on genomic data. These DoSnRKs could be grouped into three subfamilies, including 1 member of DoSnRK1, 7 of DoSnRK2, and 28 of DoSnRK3. The gene structure analysis of DoSnRK genes showed that 17 members had no introns, while 16 members contained six or more introns. The conserved domains and motifs were found in the same subfamily. The various cis-elements present in the promoter regions showed that DoSnRK genes could respond to stresses and hormones. Furthermore, the expression patterns of DoSnRK genes in eight tissues were investigated according to RNA sequencing data, indicating that multiple DoSnRK genes were ubiquitously expressed in these tissues. The transcript levels of DoSnRK genes after drought, MeJA, and ABA treatments were analyzed by quantitative real-time PCR and showed that most DoSnRK genes could respond to these stresses. Therefore, genomic characterization and expression analyses provide valuable information on DoSnRK genes for further understanding the functions of SnRKs in plants.

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.

The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli

Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.

Involvement of abscisic acid-responsive element-binding factors in cassava (Manihot esculenta) dehydration stress response

Cassava (Manihot esculenta) is a major staple food, animal feed and energy crop in the tropics and subtropics. It is one of the most drought-tolerant crops, however, the mechanisms of cassava drought tolerance remain unclear. Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) are transcription factors that regulate expression of target genes involved in plant tolerance to drought, high salinity, and osmotic stress by binding ABRE cis-elements in the promoter regions of these genes. However, there is little information about ABF genes in cassava. A comprehensive analysis of Manihot esculenta ABFs (MeABFs) described the phylogeny, genome location, cis-acting elements, expression profiles, and regulatory relationship between these factors and Manihot esculenta betaine aldehyde dehydrogenase genes (MeBADHs). Here we conducted genome-wide searches and subsequent molecular cloning to identify seven MeABFs that are distributed unevenly across six chromosomes in cassava. These MeABFs can be clustered into three groups according to their phylogenetic relationships to their Arabidopsis (Arabidopsis thaliana) counterparts. Analysis of the 5′-upstream region of MeABFs revealed putative cis-acting elements related to hormone signaling, stress, light, and circadian clock. MeABF expression profiles displayed clear differences among leaf, stem, root, and tuberous root tissues under non-stress and drought, osmotic, or salt stress conditions. Drought stress in cassava leaves and roots, osmotic stress in tuberous roots, and salt stress in stems induced expression of the highest number of MeABFs showing significantly elevated expression. The glycine betaine (GB) content of cassava leaves also was elevated after drought, osmotic, or salt stress treatments. BADH1 is involved in GB synthesis. We show that MeBADH1 promoter sequences contained ABREs and that MeBADH1 expression correlated with MeABF expression profiles in cassava leaves after the three stress treatments. Taken together, these results suggest that in response to various dehydration stresses, MeABFs in cassava may activate transcriptional expression of MeBADH1 by binding the MeBADH1 promoter that in turn promotes GB biosynthesis and accumulation via an increase in MeBADH1 gene expression levels and MeBADH1 enzymatic activity. These responses protect cells against dehydration stresses by preserving an osmotic balance that enhances cassava tolerance to dehydration stresses.

Functional analysis of Leifsonia xyli subsp. xyli membrane protein gene Lxx18460 (anti-sigma K)

BACKGROUND

Sugarcane is an important sugar and economic crop in the world. Ratoon stunting Disease (RSD) of sugarcane, caused by Leifsonia xyli subsp. xyli, is widespread in countries and regions where sugarcane is grown and also limited to sugarcane productivity. Although the whole genome sequencing of Leifsonia xyli subsp. xyli was completed, progress in understanding the molecular mechanism of the disease has been slow because it is difficult to grow in culture.

RESULTS

The Leifsonia xyli subsp. xyli membrane protein gene Lxx18460 (anti-sigma K) was cloned from the Lxx-infected sugarcane cultivar GT11 at the mature stage using RT-PCR technique, and the gene structure and expression in infected sugarcane were analyzed. The Lxx18460 gene was transformed into Nicotiana tabacum by Agrobacterium tumefaciens-mediation. The transgenic tobacco plants overexpressing Lxx18460 had lower levels in plant height, leaf area, net photosynthetic rate and endogenous hormones of IAA, ABA and GA3, as well as lower activities of three antioxidant enzymes, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) than the wild type (WT) tobacco. With the plant growth, the expression of Lxx18460 gene and protein was increased. To better understand the regulation of Lxx18460 expression, transcriptome analysis of leaves from transgenic and wild type tobacco was performed. A total of 60,222 all-unigenes were obtained through BGISEQ-500 sequencing. Compared the transgenic plants with the WT plants, 11,696 upregulated and 5949 downregulated genes were identified. These differentially expressed genes involved in many metabolic pathways including signal transduction, biosynthesis of other secondary metabolism, carbohydrate metabolism and so on. Though the data presented here are from a heterologous system, Lxx 18460 has an adverse impact on the growth of tobacco; it reduces the photosynthesis of tobacco, destroys the activity of defense enzymes, and affects the levels of endogenous hormones, which indicate that Lxx18460 may act important roles in the course of infection in sugarcane.

CONCLUSIONS

This is the first study on analyzing the function of the membrane protein gene Lxx18460 of anti-sigma K (σK) factor in Leifsonia xyli subsp. xyli. Our findings will improve the understanding of the interaction between the RSD pathogen Leifsonia xyli subsp. xyli and sugarcane. The output of this study will also be helpful to explore the pathogenesis of RSD.

Genome-wide identification and characterization of the CsSnRK2 family in Camellia sinensis

The sucrose nonfermenting 1 (SNF1)-related protein kinase 2 (SnRK2) genes play central roles in plant stress signal transduction. In this study, 8 SnRK2 genes were identified from the tea plant genome database and named CsSnRK2.1-8. Phylogenetic analysis showed that the CsSnRK2 genes were classifiable into three groups, similar to those of Arabidopsis thaliana, Oryza sativa and maize. The coding sequences (CDSs) of all CsSnRK2s were separated by eight introns, and their exon-intron organizations exhibited high similarity to those of other plants. The fluorescence of GFP fused with CsSnRK2.3 was detected in only the cytoplasm, while the rest of the proteins showed GFP signal in both the nucleus and the cytoplasm. The results of the expression patterns of the CsSnRK2 genes showed that CsSnRK2s were differentially induced by salt, polyethylene glycol (PEG) and abscisic acid (ABA) stress. Interestingly, The expression of CsSnRK2.3 was inhibited by ABA, suggesting the complicated roles of CsSnRK2s in the ABA signal transduction pathway. Some CsSnRK2 gene pairs showed significant expression change correlations under stresses, indicating that CsSnRK2s might exhibit synergistic effects of signal regulation in response to various stresses. In summary, this comprehensive analysis will facilitate further studies of the SnRK2 family of Camellia sinensis and provide useful information for the functional validation of CsSnRK2s.

Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

The energy sensor OsSnRK1a confers broad-spectrum disease resistance in rice

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) belongs to a family of evolutionary conserved kinases with orthologs in all eukaryotes, ranging from yeasts (SnF1) to mammals (AMP-Activated kinase). These kinases sense energy deficits caused by nutrient limitation or stress and coordinate the required adaptations to maintain energy homeostasis and survival. In plants, SnRK1 is a global regulator of plant metabolism and is also involved in abiotic stress responses. Its role in the response to biotic stress, however, is only starting to be uncovered. Here we studied the effect of altered SnRK1a expression on growth and plant defense in rice. OsSnRK1a overexpression interfered with normal growth and development and increased resistance against both (hemi)biotrophic and necrotrophic pathogens, while OsSnRK1a silencing in RNAi lines increased susceptibility. OsSnRK1a overexpression positively affected the salicylic acid pathway and boosted the jasmonate-mediated defense response after inoculation with the blast fungus Pyricularia oryzae. Together these findings strongly suggest OsSnRK1a to be involved in plant basal immunity and favor a model whereby OsSnRK1a acts as a master switch that regulates growth-immunity trade-offs.

Molecular Characterization and Co-expression Analysis of the SnRK2 Gene Family in Sugarcane (Saccharum officinarum L.)

In plants, both abscisic acid (ABA) dependent and independent pathways form the basis for the response to environmental stresses. Sucrose non-fermenting 1-related protein kinase 2 (SnRK2) plays a central role in plant stress signal transduction. However, complete annotation and specific expression patterns of SnRK2s in sugarcane remain unclear. For the present study, we performed a full-length cDNA library survey of sugarcane, thus identifying ten SoSnRK2 genes via phylogenetic, local BLAST methods, and various bioinformatics analyses. Phylogenetic analysis indicated division of SoSnRK2 genes into three subgroups, similar to other plant species. Gene structure comparison with Arabidopsis suggested a unique evolutionary imprint of the SnRK2 gene family in sugarcane. Both sequence alignment and structural annotation provided an overview of the conserved N-terminal and variations of the C-terminal, suggesting functional divergence. Transcript and transient expression assays revealed SoSnRK2s to be involved in the responses to diverse stress signals, and strong ABA induction of SoSnRK2s in subgroup III. Co-expression network analyses indicated the existence of both conserved and variable biological functions among different SoSnRK2s members. In summary, this comprehensive analysis will facilitate further studies of the SoSnRK2 family and provide useful information for the functional validation of SoSnRK2s.