Whole genome transcriptome analysis of rice seedling reveals alterations in Ca(2+) ion signaling and homeostasis in response to Ca(2+) deficiency

Ammonium nutrition modifies cellular calcium distribution influencing ammonium-induced growth inhibition

Proper plant growth requires balanced nutrient levels. In this study, we analyzed the relationship between ammonium (NH4+) nutrition and calcium (Ca2+) homeostasis in the leaf tissues of wild-type and mutant Arabidopsis specimens provided with different nitrogen sources (NH4+ and nitrate, NO3-). Providing plants with NH4+ as the sole nitrogen source disrupts Ca2+ homeostasis, which is essential for activating signaling pathways and maintaining the cell wall structure. The results revealed that the lower Ca2+ content in Arabidopsis leaves under NH4+ stress might result from reduced transpiration pull, which could impair root-to-shoot Ca2+ transport. Moreover, NH4+ nutrition increased the expression of genes encoding proteins responsible for exporting Ca2+ from the cytosol of leaf cells. Furthermore, overexpression of the Ca2+/H+ antiporter 1 (CAX1) gene alleviates the effects of NH4+ syndrome, including stunted growth. The oeCAX1 plants, characterized by a lower apoplastic Ca2+ level, grew better under NH4+ stress than wild-type plants. Evaluation of the mechanical properties of the leaf blades, including stiffness, strength, toughness, and extensibility, showed that the wild-type and oeCAX1 plants responded differently to the nitrogen source, highlighting the role of cell wall metabolism in inhibiting the growth of NH4+-stressed plants.

Role of calcium nutrition in plant Physiology: Advances in research and insights into acidic soil conditions - A comprehensive review

Plant mineral nutrition has immense significance for crop productivity and human well-being. Soil acidity plays a major role in determining the nutrient availability that influences plant growth. The importance of calcium (Ca) in biological processes, such as signaling, metabolism, and cell growth, underlines its critical role in plant growth and development. This review focuses on soil acidification, a gradual process resulting from cation leaching, fertilizer utilization, and drainage issues. Soil acidification significantly hampers global crop production by modifying nutrient accessibility. In acidic soils, essential nutrients, such as nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), and Ca become less accessible, establishing a correlation between soil pH and plant nutrition. Cutting-edge Ca nutrition technologies, including nanotechnology, genetic engineering, and genome sequencing, offer the potential to deliver Ca and reduce the reliance on conventional soluble fertilizers. These fertilizers not only contribute to environmental contamination but also impose economic burdens on farmers. Nanotechnology can enhance nutrient uptake, and Ca nanoparticles improve nutrient absorption and release. Genetic engineering enables the cultivation of acid-tolerant crop varieties by manipulating Ca-related genes. High-throughput technologies such as next-generation sequencing and microarrays aid in identifying the microbial structures, functions, and biosynthetic pathways involved in managing plant nutritional stress. The ultimate goal is to shed light on the importance of Ca, problems associated with soil acidity, and potential of emerging technologies to enhance crop production while minimizing the environmental impact and economic burden on farmers.

Ca2+-CBL-CIPK: a modulator system for efficient nutrient acquisition

Calcium (Ca²⁺) is a universal second messenger essential for the growth and development of plants in normal and stress situations. In plants, the proteins, CBL (calcineurin B-like) and CIPK (CBL-interacting protein kinase), form one of the important Ca²⁺ decoding complexes to decipher Ca²⁺ signals elicited by environmental challenges. Multiple interactors distinguish CBL and CIPK protein family members to form a signaling network for regulated perception and transduction of environmental signals, e.g., signals generated under nutrient stress conditions. Conservation of equilibrium in response to varying soil nutrient status is an important aspect for plant vigor and yield. Signaling processes have been reported to observe nutrient fluctuations as a signal responsible for regulated nutrient transport adaptation. Recent studies have identified downstream targets of CBL-CIPK modules as ion channels or transporters and their association in signaling nutrient disposal including potassium, nitrate, ammonium, magnesium, zinc, boron, and iron. Ca²⁺-CBL-CIPK pathway modulates ion transporters/channels and hence maintains a homeostasis of several important plant nutrients in the cytosol and sub-cellular compartments. In this article, we summarize recent literature to discuss the role of the Ca²⁺-CBL-CIPK pathway in cellular osmoregulation and homeostasis on exposure to nutrient excess or deprived soils. This further establishes a link between taking up the nutrient in the roots and its distribution and homeostasis during the generation of signal for the development and survival of plants.

Comparative Omics Analysis of Brassica napus Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles

The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of Brassica napus roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.

Magnesium Deficiency Induced Global Transcriptome Change in Citrus sinensis Leaves Revealed by RNA-Seq

Magnesium (Mg) deficiency is one of the major constraining factors that limit the yield and quality of agricultural products. Uniform seedlings of the Citrus sinensis were irrigated with Mg deficient (0 mM MgSO₄) and Mg sufficient (1 mM MgSO₄) nutrient solutions for 16 weeks. CO₂ assimilation, starch, soluble carbohydrates, TBARS content and H₂O₂ production were measured. Transcriptomic analysis of C. sinensis leaves was performed by Illumina sequencing. Our results showed that Mg deficiency decreased CO₂ assimilation, but increased starch, sucrose, TBARS content and H₂O₂ production in C. sinensis leaves. A total of 4864 genes showed differential expression in response to Mg deficiency revealed by RNA-Seq and the transcriptomic data were further validated by real-time quantitative PCR (RT-qPCR). Gene ontology (GO) enrichment analysis indicated that the mechanisms underlying Mg deficiency tolerance in C. sinensis may be attributed to the following aspects: (a) enhanced microtubule-based movement and cell cycle regulation; (b) elevated signal transduction in response to biotic and abiotic stimuli; (c) alteration of biological processes by tightly controlling phosphorylation especially protein phosphorylation; (d) down-regulation of light harvesting and photosynthesis due to the accumulation of carbohydrates; (e) up-regulation of cell wall remodeling and antioxidant system. Our results provide a comprehensive insight into the transcriptomic profile of key components involved in the Mg deficiency tolerance in C. sinensis and enrich our understanding of the molecular mechanisms by which plants adapted to a Mg deficient condition.

Elevation of cytosolic Ca2+ in response to energy deficiency in plants: the general mechanism of adaptation to low oxygen stress

Ca2+ can be released from cell compartments to the cytosol during stress conditions. We discuss here the causes of Ca2+ release under conditions of ATP concentration decline that result in the suppression of ATPases and activation of calcium ion channels. The main signaling and metabolic consequences of Ca2+ release are considered for stressed plant cells. The signaling function includes generation and spreading of calcium waves, while the metabolic function results in the activation of particular enzymes and genes. Ca2+ is involved in the activation of glutamate decarboxylase, initiating the γ-aminobutyric acid shunt and triggering the formation of alanine, processes which play a role, in particular, in pH regulation. Ca2+ activates the transcription of several genes, e.g. of plant hemoglobin (phytoglobin, Pgb) which scavenges nitric oxide and regulates redox and energy balance through the Pgb–nitric oxide cycle. This cycle involves NADH and NADPH oxidation from the cytosolic side of mitochondria, in which Ca2+- and low pH-activated external NADH and NADPH dehydrogenases participate. Ca2+ can also activate the genes of alcohol dehydrogenase and pyruvate decarboxylase stimulating hypoxic fermentation. It is concluded that calcium is a primary factor that causes the metabolic shift under conditions of oxygen deficiency.

Rice phytoglobins regulate responses under low mineral nutrients and abiotic stresses in Arabidopsis thaliana

Just like animals, plants also contain haemoglobins (known as phytoglobins in plants). Plant phytoglobins (Pgbs) have been categorized into 6 different classes, namely, Phytogb0 (Pgb0), Phytogb1 (Pgb1), Phytogb2 (Pgb2), SymPhytogb (sPgb), Leghaemoglobin (Lb), and Phytogb3 (Pgb3). Among the 6 Phytogbs, sPgb and Lb have been functionally characterized, whereas understanding of the roles of other Pgbs is still evolving. In our present study, we have explored the function of 2 rice Pgbs (OsPgb1.1 and OsPgb1.2). OsPgb1.1, OsPgb1.2, OsPgb1.3, and OsPgb1.4 displayed increased level of transcript upon salt, drought, cold, and ABA treatment. The overexpression (OX) lines of OsPgb1.2 in Arabidopsis showed a tolerant phenotype in terms of better root growth in low potassium (K+ ) conditions. The expression of the known K+ gene markers such as LOX2, HAK5, and CAX3 was much higher in the OsPgb1.2 OX as compared to wild type. Furthermore, the OsPgb1.2 OX lines showed a decrease in reactive oxygen species (ROS) production and conversely an increase in the K+ content, both in root and shoot, as compared to wild type in K+ limiting condition. Our results indicated the potential involvement of OsPgb1.2 in signalling networks triggered by the nutrient deficiency stresses.

Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea

Activation of stress tolerance mechanisms demands transcriptional reprogramming. Salt stress, a major threat to plant growth, enhances ROS production and affects transcription through modulation of miRNAs and hormones. The present study delineates salt stress ameliorating action of thiourea (TU, a ROS scavenger) in Brassica juncea and provides mechanistic link between redox, microRNA and hormones. The ameliorative potential of TU towards NaCl stress was related with its ability to decrease ROS accumulation in roots and increase Na+ accumulation in shoots. Small RNA sequencing revealed enrichment of down-regulated miRNAs in NaCl + TU treated roots, indicating transcriptional activation. Ranking analysis identified three key genes including BRX4, CBL10 and PHO1, showing inverse relationship with corresponding miRNA expression, which were responsible for TU mediated stress mitigation. Additionally, ABA level was consistently higher till 24 h in NaCl, while NaCl + TU treated roots showed only transient increase at 4 h suggesting an effective stress management. Jasmonate and auxin levels were also increased, which prioritized defence and facilitated root growth, respectively. Thus, the study highlights redox as one of the "core" components regulating miRNA and hormone levels, and also strengthens the use of TU as a redox priming agent for imparting crop resilience to salt stress.

Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India

Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.

A rice tonoplastic calcium exchanger, OsCCX2 mediates Ca2+/cation transport in yeast

In plant cell, cations gradient in cellular compartments is maintained by synergistic action of various exchangers, pumps and channels. The Arabidopsis exchanger family members (AtCCX3 and AtCCX5) were previously studied and belong to CaCA (calcium cation exchangers) superfamily while none of the rice CCXs has been functionally characterized for their cation transport activities till date. Rice genome encode four CCXs and only OsCCX2 transcript showed differential expression under abiotic stresses and Ca(2+) starvation conditions. The OsCCX2 localized to tonoplast and suppresses the Ca(2+) sensitivity of K667 (low affinity Ca(2+) uptake deficient) yeast mutant under excess CaCl2 conditions. In contrast to AtCCXs, OsCCX2 expressing K667 yeast cells show tolerance towards excess Na(+), Li(+), Fe(2+), Zn(2+) and Co(2+) and suggest its ability to transport both mono as well as divalent cations in yeast. Additionally, in contrast to previously characterized AtCCXs, OsCCX2 is unable to complement yeast trk1trk2 double mutant suggesting inability to transport K(+) in yeast system. These finding suggest that OsCCX2 having distinct metal transport properties than previously characterized plant CCXs. OsCCX2 can be used as potential candidate for enhancing the abiotic stress tolerance in plants as well as for phytoremediation of heavy metal polluted soil.

Role of Protein Tyrosine Phosphatases in Plants

Reversible protein phosphorylation is a crucial regulatory mechanism that controls many biological processes in eukaryotes. In plants, phosphorylation events primarily occur on serine (Ser) and threonine (Thr) residues, while in certain cases, it was also discovered on tyrosine (Tyr) residues. In contrary to plants, extensive reports on Tyr phosphorylation regulating a large numbers of biological processes exist in animals. Despite of such prodigious function in animals, Tyr phosphorylation is a least studied mechanism of protein regulation in plants. Recently, various chemical analytical procedures have strengthened the view that Tyr phosphorylation is equally prevalent in plants as in animals. However, regardless of Tyr phosphorylation events occuring in plants, no evidence could be found for the existence of gene encoding for Tyr phosphorylation i.e. the typical Tyr kinases. Various methodologies have suggested that plant responses to stress signals and developmental processes involved modifications in protein Tyr phosphorylation. Correspondingly, various reports have established the role of PTPs (Protein Tyrosine Phosphatases) in the dephosphorylation and inactivation of mitogen activated protein kinases (MAPKs) hence, in the regulation of MAPK signaling cascade. Besides this, many dual specificity protein phosphatases (DSPs) are also known to bind starch and regulate starch metabolism through reversible phosphorylation. Here, we are emphasizing the significant progress on protein Tyr phosphatases to understand the role of these enzymes in the regulation of post-translational modification in plant physiology and development.