Transcriptional analyses of two soybean cultivars under salt stress

Genome-wide analysis of the SCAMPs gene family of soybean and functional identification of GmSCAMP5 in salt tolerance

The effect of salt damage on plants is mainly caused by the toxic effect of Na+. Studies showed that the secretory carrier membrane proteins were associated with the Na+ transport. However, the salt tolerance mechanism of secretory carrier protein (SCAMP) in soybean was yet to be defined. In this study, ten potential SCAMP genes distributed in seven soybean chromosomes were identified in the soybean genome. The phylogenetic tree of SCAMP domain sequences of several plants can divide SCAMPs into two groups. Most GmSCAMPs genes contained multiple Box4, MYB and MYC cis-elements indicated they may respond to abiotic stresses. We found that GmSCAMP1, GmSCAMP2 and GmSCAMP4 expressed in several tissues and GmSCAMP5 was significantly induced by salt stress. GmSCAMP5 showed the same expression patterns under NaCl treatment in salt-tolerant and salt-sensitive soybean varieties, but the induced time of GmSCAMP5 in salt-tolerant variety was earlier than that of salt-sensitive variety. To further study the effect of GmSCAMP5 on the salt tolerance of soybean plants, compared to GmSCAMP5-RNAi and EV-Control plants, GmSCAMP5-OE had less wilted leave and higher SPAD value. Compared to empty vector control, less trypan blue staining was observed in GmSCAMP5-OE leaves while more staining in GmSCAMP5-RNAi leaves. The Na+ of GmSCAMP5-RNAi plants leaves under NaCl stress were significantly higher than that in EV-Control plants, while significantly lower Na+ in GmSCAMP5-OE plants than in that EV-Control plants. The contents of leaves K+ of GmSCAMP5-RNAi, EV-Control, and GmSCAMP5-OE plants under NaCl stress were opposite to that of leaves Na+ content. Finally, salt stress-related genes NHX1, CLC1, TIP1, SOD1, and SOS1 in transformed hairy root changed significantly compared with the empty control. The research will provide novel information for study the molecular regulation mechanism of soybean salt tolerance.

Starch and Sucrose Metabolism and Plant Hormone Signaling Pathways Play Crucial Roles in Aquilegia Salt Stress Adaption

Salt stress is one of the main abiotic stresses that strongly affects plant growth. Clarifying the molecular regulatory mechanism in ornamental plants under salt stress is of great significance for the ecological development of saline soil areas. Aquilegia vulgaris is a perennial with a high ornamental and commercial value. To narrow down the key responsive pathways and regulatory genes, we analyzed the transcriptome of A. vulgaris under a 200 mM NaCl treatment. A total of 5600 differentially expressed genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis pointed out that starch and sucrose metabolism and plant hormone signal transduction were significantly improved. The above pathways played crucial roles when A. vulgaris was coping with salt stress, and their protein-protein interactions (PPIs) were predicted. This research provides new insights into the molecular regulatory mechanism, which could be the theoretical basis for screening candidate genes in Aquilegia.

Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress

Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.

Unfolding molecular switches for salt stress resilience in soybean: recent advances and prospects for salt-tolerant smart plant production

The increasing sodium salts (NaCl, NaHCO3, NaSO4 etc.) in agricultural soil is a serious global concern for sustainable agricultural production and food security. Soybean is an important food crop, and their cultivation is severely challenged by high salt concentration in soils. Classical transgenic and innovative breeding technologies are immediately needed to engineer salt tolerant soybean plants. Additionally, unfolding the molecular switches and the key components of the soybean salt tolerance network are crucial for soybean salt tolerance improvement. Here we review our understandings of the core salt stress response mechanism in soybean. Recent findings described that salt stress sensing, signalling, ionic homeostasis (Na⁺/K⁺) and osmotic stress adjustment might be important in regulating the soybean salinity stress response. We also evaluated the importance of antiporters and transporters such as Arabidopsis K⁺ Transporter 1 (AKT1) potassium channel and the impact of epigenetic modification on soybean salt tolerance. We also review key phytohormones, and osmo-protectants and their role in salt tolerance in soybean. In addition, we discuss the progress of omics technologies for identifying salt stress responsive molecular switches and their targeted engineering for salt tolerance in soybean. This review summarizes recent progress in soybean salt stress functional genomics and way forward for molecular breeding for developing salt-tolerant soybean plant.

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detect every gene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models and human-derived samples.

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection

To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detect every gene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. At the individual-gene level, EGR3 was significantly upregulated in infected cells. Similar activation in T-cells and fibroblasts in infected lung could explain the T-cell anergy and eventual fibrosis seen in SARS-CoV-1 infection. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models, and human-derived samples.

Progress in understanding salt stress response in plants using biotechnological tools

Salinization is a worldwide environmental problem, which is negatively impacting crop yield and thus posing a threat to the world's food security. Considering the rising threat of salinity, it is need of time, to understand the salt tolerant mechanism in plants and find avenues for the development of salinity resistant plants. Several plants tolerate salinity in a different manner, thereby halophytes and glycophytes evolved altered mechanisms to counter the stress. Therefore, in this review article, physiological, metabolic, and molecular aspects of the plant adaptation to salt stress have been discussed. The conventional breeding techniques for developing salt tolerant plants has not been much successful, due to its multigenic trait. The inflow of data from plant sequencing projects and annotation of genes led to the identification of many putative genes having a role in salt stress. The bioinformatics tools provided preliminary information and were helpful for making salt stress-specific databases. The microRNA identification and characterization led to unraveling the finer intricacies of the network. The transgenic approach finally paved a way for overexpressing some important genes viz. DREB, MYB, COMT, SOS, PKE, NHX, etc. conferred salt stress tolerance. In this review, we tried to show the effect of salinity on plants, considering ion homeostasis, antioxidant defense response, proteins involved, possible utilization of transgenic plants, and bioinformatics for coping with this stress factor. An overview of previous studies related to salt stress is presented in order to assist researchers in providing a potential solution for this increasing environmental threat.

HDAC inhibitor affects soybean miRNA482bd expression under salt and osmotic stress

MicroRNAs (miRNAs) are small non-coding molecules that modulate gene expression through targeting mRNA by specific-sequence cleavage, translation inhibition, or transcriptional regulation. miRNAs are key molecules in regulatory networks in abiotic stresses such as salt stress and water deficit in plants. Throughout the world, soybean is a critical crop, the production of which is affected by environmental stress conditions. In this study, RNA-Seq libraries from leaves of soybean under salt treatment were analyzed. 17 miRNAs and 31 putative target genes were identified with inverse differential expression patterns, indicating miRNA-target interaction. The differential expression of six miRNAs, including miR482bd-5p, and their potential targets, were confirmed by RT-qPCR. The miR482bd-5p expression was repressed, while its potential HEC1 and BAK1 targets were increased. Polyethylene glycol experiment was used to simulate drought stress, and miR482bd-5p, HEC1, and BAK1 presented a similar expression pattern, as found in salt stress. Histone modifications occur in response to abiotic stress, where histone deacetylases (HDACs) can lead to gene repression and silencing. The miR482bd-5p epigenetic regulation by histone deacetylation was evaluated by using the SAHA-HDAC inhibitor. The miR482bd-5p was up-regulated, and HEC1 was down-regulated under SAHA-salt treatment. It suggests an epigenetic regulation, where the miRNA gene is repressed by HDAC under salt stress, reducing its transcription, with an associated increase in the HEC1 target expression.

Comparative transcriptome profiling of rice colonized with beneficial endophyte, Piriformospora indica, under high salinity environment

The salinity stress tolerance in plants has been studied enormously, reflecting its agronomic relevance. Despite the extensive research, limited success has been achieved in relation to the plant tolerance mechanism. The beneficial interaction between Piriformospora indica and rice could essentially improve the performance of the plant during salt stress. In this study, the transcriptomic data between P. indica treated and untreated rice roots were compared under control and salt stress conditions. Overall, 661 salt-responsive differentially expressed genes (DEGs) were detected with 161 up- and 500 down-regulated genes in all comparison groups. Gene ontology analyses indicated the DEGs were mainly enriched in "auxin-activated signaling pathway", "water channel activity", "integral component of plasma membrane", "stress responses", and "metabolic processes". Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the DEGs were primarily related to "Zeatin biosynthesis", "Fatty acid elongation", "Carotenoid biosynthesis", and "Biosynthesis of secondary metabolites". Particularly, genes related to cell wall modifying enzymes (e.g. invertase/pectin methylesterase inhibitor protein and arabinogalactans), phytohormones (e.g. Auxin-responsive Aux/IAA gene family, ent-kaurene synthase, and 12-oxophytodienoate reductase) and receptor-like kinases (e.g. AGC kinase and receptor protein kinase) were induced in P. indica colonized rice under salt stress condition. The differential expression of these genes implies that the coordination between hormonal crosstalk, signaling, and cell wall dynamics contributes to the higher growth and tolerance in P. indica-inoculated rice. Our results offer a valuable resource for future functional studies on salt-responsive genes that should improve the resilience and adaptation of rice against salt stress.