Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress.

The adzuki bean Vigna angularis (Wild.) is an important leguminous crop cultivated mainly for food purposes in Asian countries; it represents a source of carbohydrates, digestible proteins, minerals, and vitamins. Aquaporins (AQPs) are crucial membrane proteins involved in the transmembrane diffusion of water and small solutes in all living organisms, including plants. In this study, we used the whole genome sequence of the adzuki bean for in silico analysis to comprehensively identify 40 Vigna angularis aquaporin (VaAQP) genes and reveal how these plants react to drought stress. VaAQPs were compared with AQPs from other closely-related leguminous plants, and the results showed that mustard (Brassica rapa) (59), barrel medic (Medicago truncatula) (46), soybean (Glycine max) (66), and common bean (Phaseolus vulgaris L.) (41) had more AQP genes. Phylogenetic analysis revealed that forty VaAQPs belong to five subfamilies, with the VaPIPs (fifteen) subfamily the largest, followed by the VaNIPs (ten), VaTIPs (ten), VaSIPs (three), and VaXIPs (two) subfamilies. Furthermore, all AQP subcellular locations were found at the plasma membrane, and intron-exon analysis revealed a relationship between the intron number and gene expression, duplication, evolution, and diversity. Among the six motifs identified, motifs one, two, five, and six were prevalent in VaTIP, VaNIP, VaPIP, and VaXIP, while motifs one, three, and four were not observed in VaPIP1-3 and VaPIP1-4. Under drought stress, two of the VaAQPs (VaPIP2-1 and VaPIP2-5) showed significantly higher expression in the root tissue while the other two genes (VaPIP1-1 and VaPIP1-7) displayed variable expression in leaf tissue. This finding revealed that the selected VaAQPs might have unique molecular functions linked with the uptake of water under drought stress or in the exertion of osmoregulation to transport particular substrates rather than water to protect plants from drought. This study presents the first thorough investigation of VaAQPs in adzuki beans, and it reveals the transport mechanisms and related physiological processes that may be utilized for the development of drought-tolerant adzuki bean cultivars.

Significance of solute specificity, expression, and gating mechanism of tonoplast intrinsic protein during development and stress response in plants.

Tonoplast intrinsic proteins (TIPs), belonging to the aquaporin family, are transmembrane channels located mostly at the tonoplast of plant cells. The TIPs are known to transport water and many other small solutes such as ammonia, urea, hydrogen peroxide, and glycerol. In the present review, phylogenetic distribution, structure, transport dynamics, gating mechanism, sub-cellular localization, tissue-specific expression, and co-expression of TIPs are discussed to define their versatile role in plants. Based on the phylogenetic distribution, TIPs are classified into five distinct groups with aromatic-arginine (Ar/R) selectivity filters, typical pore-morphology, and tissue-specific gene expression patterns. The tissue-specific expression of TIPs is conserved among diverse plant species, more particularly for TIP3s, which are expressed exclusively in seeds. Studying TIP3 evolution will help to understand seed development and germination. The solute specificity of TIPs plays an imperative role in physiological processes like stomatal movement and vacuolar sequestration as well as in alleviating environmental stress. TIPs also play an important role in growth and developmental processes like radicle protrusion, anther dehiscence, seed germination, cell elongation, and expansion. The gating mechanism of TIPs regulates the solute flow in response to external signals, which helps to maintain the physiological functions of the cell. The information provided in this review is a base to explore TIP's potential in crop improvement programs.

Significance of silicon uptake, transport, and deposition in plants.

Numerous studies have shown the beneficial effects of silicon (Si) for plant growth, particularly under stress conditions, and hence a detailed understanding of the mechanisms of its uptake, subsequent transport, and accumulation in different tissues is important. Here, we provide a thorough review of our current knowledge of how plants benefit from Si supplementation. The molecular mechanisms involved in Si transport are discussed and we highlight gaps in our knowledge, particularly with regards to xylem unloading and transport into heavily silicified cells. Silicification of tissues such as sclerenchyma, fibers, storage tissues, the epidermis, and vascular tissues are described. Silicon deposition in different cell types, tissues, and intercellular spaces that affect morphological and physiological properties associated with enhanced plant resilience under various biotic and abiotic stresses are addressed in detail. Most Si-derived benefits are the result of interference in physiological processes, modulation of stress responses, and biochemical interactions. A better understanding of the versatile roles of Si in plants requires more detailed knowledge of the specific mechanisms involved in its deposition in different tissues, at different developmental stages, and under different environmental conditions.

Structural assessment of OsNIP2;1 highlighted critical residues defining solute specificity and functionality of NIP class aquaporins.

INTRODUCTION: Nodulin-26-like intrinsic proteins (NIPs) are integral membrane proteins belonging to the aquaporin family, that facilitate the transport of neutral solutes across the bilayer. The OsNIP2;1 a member of NIP-III class of aquaporins is permeable to beneficial elements like silicon and hazardous arsenic. However, the atomistic cross-talk of these molecules traversing the OsNIP2;1 channel is not well understood. OBJECTIVE: Due to the lack of genomic variation but the availability of high confidence crystal structure, this study aims to highlight structural determinants of metalloid permeation through OsNIP2;1. METHODS: The molecular simulations, combined with site-directed mutagenesis were used to probe the role of specific residues in the metalloid transport activity of OsNIP2;1. RESULTS: We drew energetic landscape of OsNIP2;1, for silicic and arsenous acid transport. Potential Mean Force (PMF) construction illuminate three prominent energetic barriers for metalloid passage through the pore. One corresponds to the extracellular molecular entry in the channel, the second located on ar/R filter, and the third size constriction in the cytoplasmic half. Comparative PMF for silicic acid and arsenous acid elucidate a higher barrier for silicic acid at the cytoplasmic constrict resulting in longer residence time for silicon. Furthermore, our simulation studies explained the importance of conserved residues in loop-C and loop-D with a direct effect on pore dynamics and metalloid transport. Next we assessed contribution of predicted key residues for arsenic uptake, by functional complementation in yeast. With the aim of reducing arsenic uptake while maintaining beneficial elements uptake, we identified novel OsNIP2;1 mutants with substantial reduction in arsenic uptake in yeast. CONCLUSION: We provide a comprehensive assessment of pore lining residues of OsNIP2;1 with respect to metalloid uptake. The findings will expand mechanistic understanding of aquaporin's metalloid selectivity and facilitate variant interpretation to develop novel alleles with preference for beneficial metalloid species and reducing hazardous ones.

Unveiling silicon-mediated cadmium tolerance mechanisms in mungbean (Vigna radiata (L.) Wilczek): Integrative insights from gene expression, antioxidant responses, and metabolomics.

Cadmium (Cd), one of the most phytotoxic heavy metals, is a major contributor to yield losses in several crops. Silicon (Si) is recognized for its vital role in mitigating Cd toxicity, however, the specific mechanisms governing this mitigation process are still not fully understood. In the present study, the effect of Si supplementation on mungbean (Vigna radiata (L.) Wilczek) plants grown under Cd stress was investigated to unveil the intricate pathways defining Si derived stress tolerance. Non-invasive leaf imaging technique revealed improved growth, biomass, and photosynthetic efficiency in Si supplemented mungbean plants under Cd stress. Further, physiological and biochemical analysis revealed Si mediated increase in activity of glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT) enzymes involved in reactive oxygen species (ROS) metabolism leading to mitigation of cellular damage and oxidative stress. Untargeted metabolomic analysis using liquid chromatography coupled with mass spectrometry (LC-MS/MS) provided insights into Si mediated changes in metabolites and their respective pathways under Cd stress. Alteration in five different metabolic pathways with major changes in flavanols and flavonoids biosynthesis pathway which is essential for controlling plants antioxidant defense system and oxidative stress management were observed. The information reported here about the effects of Si on photosynthetic efficiency, antioxidant responses, and metabolic changes will be helpful in understanding the Si-mediated resistance to Cd stress in plants.

Silicon, a quasi-essential element: Availability in soil, fertilizer regime, optimum dosage, and uptake in plants.

The essentiality of silicon (Si) has always been a matter of debate as it is not considered crucial for the lifecycles of most plants. But beneficial effects of endogenous Si and its supplementation have been observed in many plants. Silicon plays a pivotal role in alleviating the biotic and abiotic stress in plants by acting as a physical barrier as well as affecting molecular pathways involved in stress tolerance, thus widely considered as "quasi-essential". In soil, most of Si is found in complex forms as mineral silicates which is not available for plant uptake. Monosilicic acid [Si(OH)4] is the only plant-available form of silicon (PAS) present in the soil. The ability of a plant to uptake Si is positively correlated with the PAS concentration of the soil. Since many cultivated soils often lack a sufficient amount of PAS, it has become common practice to supplement Si through the use of Si-based fertilizers in various crop cultivation systems. This review outlines the use of natural and chemical sources of Si as fertilizer, different regimes of Si fertilization, and conclude by identifying the optimum concentration of Si required to observe the beneficial effects in plants. Also, the different mathematical models defining the mineral dynamics for Si uptake at whole plant scale considering various natural factors like plant morphology, mineral distribution, and transporter expression have been discussed. Information provided here will further help in increasing understanding of Si role and thereby facilitate efficient exploration of the element as a fertilizer in crop production.

Identification of VrNIP2-1 aquaporin with novel selective filter regulating the transport of beneficial as well as hazardous metalloids in mungbean (Vigna radiata L.).

Nodulin 26-like intrinsic protein (NIP) subfamily of aquaporins (AQPs) in plants, is known to be involved in the uptake of metalloids including boron, germanium (Ge), arsenic (As), and silicon (Si). In the present study, a thorough evaluation of 55 AQPs found in the mungbean genome, including phylogenetic distribution, sequence homology, expression profiling, and structural characterization, contributed to the identification of VrNIP2-1 as a metalloid transporter. The pore-morphology of VrNIP2-1 was studied using molecular dynamics simulation. Interestingly, VrNIP2-1 was found to harbor an aromatic/arginine (ar/R) selectivity filter formed with ASGR amino acids instead of GSGR systematically reported in metalloid transporters (NIP2s) in higher plants. Evaluation of diverse cultivars showed a high level of Si accumulation in leaves indicating functional Si transport in mungbean. In addition, heterologous expression of VrNIP2-1 in yeast revealed As(III) and GeO2 transport activity. Similarly, VrNIP2-1 expression in Xenopus oocytes confirmed its Si transport ability. The metalloid transport activity with unique structural features will be helpful to better understand the solute specificity of NIP2s in mungbean and related pulses. The information provided here will also serve as a basis to improve Si uptake while restricting hazardous metalloids like As in plants.

Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Phaseolus vulgaris L.) Through Genotyping-by-Sequencing.

Throughout the ages, the common bean has been consumed by humanity as an important food staple crop and source of nutrition on a global scale. Since its domestication, a wide spectrum of phenotypic and genotypic investigations have been carried out to unravel the potential of this crop and to understand the process of nutrient accumulation along with other desirable characteristics. The common bean is one of the essential legume crops due to its high protein and micronutrient content. The balance in micronutrients is critical for the growth and development of plants as well as humans. Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Magnesium (Mg), Calcium (Ca), and Molybdenum (Mo) are some of the important micronutrients present in legumes. Thus, we aimed to investigate the quantitative trait loci's (QTLs)/single nucleotide polymorphisms (SNPs) to identify the candidate genes associated with micronutrients through genotyping by sequencing (GBS). In our investigation, through GBS we identified SNPs linked with traits and assessed seven micronutrients in 96 selected common bean genotypes for screening nutritionally rich genotypes. Among 96399 SNPs total identified through GBS, 113 SNPs showed significant phenotypic variance, ranging from 13.50 to 21.74%. SNPs associated with most of the seed micronutrients (Mg, Mn, Fe, Ca, Cu) were found on chr3 & chr11 (Mg, Mn, Mo, Ca, Zn). The findings from this study could be used for haplotype-based selection of nutritionally rich genotypes and for marker-assisted genetic enhancement of the common bean. Further, the identified SNPs for candidate genes/transporters associated with micronutrient content may pave the way for the enrichment of seeds by employing genomics-assisted breeding programs.

Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle.

Silicon (Si), a quasi-essential element for plants, is abundant in the soil typically as insoluble silicate forms. However, plants can uptake Si only in the soluble form of monosilicic acid. Production of monosilicic acid by rock-weathering mostly depends on temperature, pH, redox-potential, water-content, and microbial activities. In the present review, approaches involved in the efficient exploration of silicate solubilizing bacteria (SSB), its potential applications, and available technological advances are discussed. Present understanding of Si uptake, deposition, and subsequent benefits to plants has also been discussed. In agricultural soils, pH is found to be one of the most critical factors deciding silicate solubilization and the formation of different Si compounds. Numerous studies have predicted the role of Indole-3-Acetic Acid (IAA) and organic acids produced by SSB in silicate solubilization. In this regard, approaches for the isolation and characterization of SSB, quantification of IAA, and subsequent Si solubilization mechanisms are addressed. Phylogenetic evaluation of previously reported SSB showed a highly diverse origin which provides an opportunity to study different mechanisms involved in Si solubilization. Soil biochemistry in concern of silicon availability, microbial activity and silicon mediated changes in plant physiology are addressed. In addition, SSB's role in Si-biogeochemical cycling is summarized. The information presented here will be helpful to explore the potential of SSB more efficiently to promote sustainable agriculture.