Transcriptional networks revealed late embryogenesis abundant genes regulating drought mitigation in aromatic Keteki Joha rice.

Climate change has become increasingly intertwined with the occurrence and severity of droughts. As global temperatures rise due to greenhouse gas emissions, weather patterns are altered, leading to shifts in precipitation levels and distribution. These exacerbate the risk of drought in many regions, with potentially devastating consequences. A comprehensive transcriptome analysis was performed on Keteki Joha, an aromatic rice from North East India, with the aim of elucidating molecular responses to drought. Numerous genes linked to drought were activated, with both ABA-dependent and ABA-independent pathways playing crucial roles. Upregulated genes were enriched with gene ontology terms with response to abscisic acid and abscisic acid-activated signalling pathway, suggesting the existence of an ABA-dependent pathway for drought mitigation. The upregulated genes were also enriched with responses to stress, water, heat, jasmonic acid, and hydrogen peroxide, indicating the presence of an ABA-independent pathway alongside the ABA-dependent mechanism. Weighted Correlation Network Analysis (WGCNA) identified 267 genes that specifically govern drought mitigation in Keteki Joha. The late embryogenesis abundant (LEA) gene family emerges as the most overrepresented in both RNA sequencing data and WGCNA analysis, suggesting their dominant role in mitigating drought. Notably, 31 LEA genes were induced in seedlings and 32 in mature stages under drought stress. The LEA3-1, LEA14/WSI18, RAB16A, RAB16B, DHN1, DHN6, LEA1, LEA3, LEA17, and LEA33 exhibited and established co-expression with numerous other drought stress-related genes, indicating their inseparable role in alleviating drought. Consequently, LEA genes have been proposed to be primary and crucial responders to drought in Keteki Joha.

Biochemical and molecular properties of Boro rice (Oryza sativa L.) cultivars under abiotic stresses.

The present investigation was conducted so as to unravel the various underlying antioxidant enzyme and non-enzyme defence mechanisms in some selected Boro rice cultivars that differ in temperature stress tolerance. Oxidative injury under heat and cold stress, H2O2 level showed a decline in roots and shoots of Boro in stressed condition whilst significant rise in the susceptible varieties was observed under both the stresses. However, susceptible varieties, such as Disang (shoots), Moricha (shoots) and China Boro (roots), showed a decreased H2O2 content at recovery. Under cold stress, roots and shoots of Boro and Laal Bihari showed a decreased level of lipid peroxidises and Boro and Kolong under heat stress. In contrast, significant enhancement of lipid peroxidase was revealed in the susceptible varieties. Remarkable increase in non-enzymatic antioxidants like proline, glutathione and ascorbate content was seen in the shoots of Boro in the treated and the recovery conditions. On the other hand, in enzymatic antioxidants like ascorbate peroxidase, guaiacol peroxidase, superoxide dismutase, catalase, and glutathione reductase activity, marked enhancement in ascorbate peroxidase activity was seen in the roots and the shoots of Boro and Kolong in treated and recovery samples and decreased in Swarnabh under heat stress. The guaiacol peroxidase activity of roots and shoots increased in Boro and Kolong under heat stress, and decreased in China boro and Swarnabh. The superoxide dismutase activity in the roots and shoot of Boro increased significantly under both the stress conditions in treated and recovery. Root and shoots of Swarnabh and Moricha showed decline in SOD activity in stressed conditions. The catalase activity in the case of Boro, showed a significant increase in both its roots and shoots under cold and heat stresses in the treated and the recovery samples. Moreover, under heat stress, the root and the shoots of Boro and Kolong showed the maximum glutathione activity, whilst Swarnabh and China Boro showed reduced glutathione activity at 96 h and recovery. On the other hand, the gene expression pattern of the cold-responsive genes (OsHAN1/OsCYP9B4 and FeSOD1) showed significant upregulation in the tolerant than the sensitive cultivars. Similarly, heat-responsive genes (OsTT1/OsPAB1 and OsHsfC1b) are also highly upregulated in the tolerant than the susceptible ones. Thus, the findings would provide a thorough insight into various non-enzymatic and enzymatic antioxidants and stress-responsive genes of Boro rice that could help in the future rice breeding programmes for cold and heat stresses.

Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses.

AP2/ERF (APETALA2/Ethylene Response Factor) is a family of transcription factors that play essential roles in regulating gene expression in response to various environmental stimuli, including biotic and abiotic stresses, hormone signaling, and developmental processes. Pisum sativum (L.), commonly known as garden pea, is a winter crop sensitive to high temperatures and can also be affected by extreme cold and drought conditions. This study performed a genome-wide analysis of AP2/ERF genes and identified 153 AP2/ERF genes in P. sativum. Based on the conserved AP2/ERF domain and sequence homology, they were classified into AP2 (APETALA2), ERF (Ethylene Response Factor), DREB (Dehydration responsive element-binding), RAV (Related to Abscisic Acid Insensitive 3/ Viviparous 1) and Soloist subfamily. The DREB and ERF subfamily were further divided into groups A1-6 and B1-B6. Tandem and segmental duplication events were more frequent in the ERF subfamily, which can have important implications for their evolution and functional diversification. Under cold stress, the expression of DREB1A was highly induced in leaves, whereas DREB1B was suppressed. Similarly, the DREB2A, DREB2C, DREB2E, and DREB2F were induced in leaves under drought stress. The putative target genes of AP2/ERF transcription factors are highly diversified, suggesting that they play essential roles in various physiological responses in plants, including responses to biotic and abiotic stresses as well as developmental processes. Thus, this study of AP2/ERF genes and their functions provides valuable insight into how P. sativum responds to different environmental conditions, including cold and drought stresses.

Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice.

Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. Under severe Fe2+ toxicity, reactive oxygen species (ROS) are crucial, although molecular mechanisms and associated ROS homeostasis genes are still unknown. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Under severe Fe2+ toxicity, the biosynthesis of amino acids, RNA degradation, and glutathione metabolism were induced, whereas phenylpropanoid biosynthesis, photosynthesis, and fatty acid elongation were inhibited. The mitochondrial iron transporter (OsMIT), vacuolar iron transporter 2 (OsVIT2), ferritin (OsFER), vacuolar mugineic acid transporter (OsVMT), phenolic efflux zero1 (OsPEZ1), root meander curling (OsRMC), and nicotianamine synthase (OsNAS3) were upregulated in different tissues, suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. Catalase (CAT), glutathione (GSH), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were upregulated. Moreover, abiotic stress-responsive transcription factors, no apical meristem (NAC), myeloblastosis (MYB), auxin response factor (ARF), basic helix-loop-helix (bZIP), WRKY, and C2H2-zinc finger protein (C2H2-ZFP) were also upregulated. Accordingly, ROS homeostasis has been proposed as an essential defense mechanism under such conditions. Thus, the current study may enrich the understanding of Fe-homeostasis in rice.

Genome-wide analysis of fluoride exporter genes in plants.

Fluoride exporter genes (FEX) are known for the expulsion of cytoplasmic fluoride, thus preventing fluoride toxicity in plants. In this study, 31 FEX genes were identified across 19 plant species. Camphor Resistance (CrcB) domain was found to be present in all the identified FEX genes in plants. FEX genes were sequentially very conserved among the plants and are located mostly in chloroplast and mitochondria. The tertiary structure (3D) of AtFEX1 suggests that FEX genes of plants possess pore I and pore II, necessary for fluoride export. The TTFSGWNQ and GCLSTVSTF motifs were found to be well conserved in pore I and pore II. Phenylalanine (Phe/F) was also present in both the motifs, necessary for fluoride ions recognition and export. Cis-acting analysis in promoter sequences of plant FEX revealed several elements associated with various functions such as phytohormone signaling, integrating biotic and abiotic stress responses in plants. Prolong fluoride exposure causes necrosis in young leaves in Vigna radiata. Expression of VrFEX1 and VrFEX2 were highly induced under exogenous fluoride, thus suggesting a possible role in fluoride detoxification. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02677-z.

Physio-biochemical and molecular assessment of Iron (Fe2+) toxicity responses in contrasting indigenous aromatic Joha rice cultivars of Assam, India.

Iron (Fe) toxicity is one of the major abiotic stresses which limits the yield of lowland rice. This study aims to investigate the physiological, biochemical, and molecular aspects of two contrasting aromatic Joha rice, viz., Keteki and Kola Joha of Assam. Oxidative damage caused due to Fe2+ toxicity was quantitatively determined. Fe2+ toxicity in the growth medium increases the level of ROS and anti-oxidative enzyme activity. Along with the aforementioned damage caused due to Fe2+ toxicity, chlorophyll content decreases in both the rice varieties. Detection of Fe3+ and Fe2+ was also conducted by Perls' Prussian and Turnbull blue method, respectively. In addition, spectrophotometric quantification of Fe2+ was determined by 2, 2'-Bipyridyl (Bpy). Above 2.5 mM, Fe2+ toxicity was found to be lethal in rice seedlings affecting their total growth and biomass. Gene expression analysis of iron-regulated transporter 1 (OsIRT1), Yellow Stripe-Like 15 (OsYSL15), and ferritin 1 (OsFer1) revealed the differential gene expression over a time period of Fe2+ toxicity. Our study suggested that the different parameters which are considered here can be helpful for the better understanding of how aromatic Joha rice performed under Fe2+ toxicity which can also help to reveal broader aspects that how gene players are involved in the iron homeostasis mechanism in Joha rice in coming future.

Chelators of iron and their role in plant's iron management.

Proper transport of metal and their homeostasis is very crucial for the growth and development of plants. Plants root are the primary organs which comes in contact with the stress and thus few modifications occurs, often determining the nutrient efficiency or sometimes as a stress tolerance mechanism. Plant utilizes two strategies for the uptake of iron viz, strategy I-reduction based and strategy II-chelation based. In this review we attempted for a better understanding of how the chelators acts in the mechanism of iron uptake from soils to plants and how iron is distributed in the plants.

Genome-wide analysis of magnesium transporter genes in Solanum lycopersicum.

Magnesium (Mg) is an important micronutrient for various physiological processes in plants. In this study, putative Magnesium Transporter (MGT) genes have been identified in Solanum lycopersicum, Solanum tuberosum, Brachypodium distachyon, Fagaria vesca, Brassica juncea and were classified into 5 distinct groups based on their sequence homology. MGT genes are very diverse and possess very low sequence identity within its family. However, the Gly-Met-Asn (GMN) signature motif is present in most of the genes which are believed to be essential for Mg2+ recognition. In S. lycopersicum, different physiological root growth pattern was observed in both Mg excess and deficient conditions. Quantitative RT-PCR gene expression study shows that most of the SlMGT genes were upregulated in response to Mg deficient condition.

Morpho-physiological analysis of tolerance to aluminum toxicity in rice varieties of North East India.

Aluminum (Al) is the third most abundant metal in earth crust, whose chemical form is mainly dependent on soil pH. The most toxic form of Al with respect to plants is Al3+, which exists in soil pH <5. Acidic soil significantly limits crop production mainly due to Al3+ toxicity worldwide, impacting approximately 50% of the world's arable land (in North-Eastern India 80% soil are acidic). Al3+ toxicity in plants ensues root growth inhibition leading to less nutrient and water uptake impacting crop productivity as a whole. Rice is one of the chief grains which constitutes the staple food of two-third of the world population including India and is not untouched by Al3+ toxicity. Al contamination is a critical constraint to plant production in agricultural soils of North East India. 24 indigenous Indica rice varieties (including Badshahbhog as tolerant check and Mashuri as sensitive check) were screened for Al stress tolerance in hydroponic plant growth system. Results show marked difference in growth parameters (relative growth rate, Root tolerance index, fresh and dry weight of root) of rice seedlings due to Al (100 µM) toxicity. Al3+ uptake and lipid peroxidation level also increased concomitantly under Al treatment. Histochemical assay were also performed to elucidate uptake of aluminum, loss of membrane integrity and lipid peroxidation, which were found to be more in sensitive genotypes at higher Al concentration. This study revealed that aluminum toxicity is a serious harmful problem for rice crop productivity in acid soil. Based on various parameters studied it's concluded that Disang is a comparatively tolerant variety whereas Joymati a sensitive variety. Western blot hybridization further strengthened the claim, as it demonstrated more accumulation of Glutathione reductase (GR) protein in Disang rice variety than Joymati under stressed condition. This study also observed that the emergence of lethal toxic symptoms occurs only after 48h irrespective of the dose used in the study.

Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants.

Tonoplast intrinsic proteins (TIPs) play a vital role in water transport across membranes. In the present study, we performed a comparative analysis of TIP genes in ten plant species including both monocots and dicots. A total of 100 TIP aquaporin genes were identified, and their relationships among the plant species were analyzed. Phylogenetic analysis was performed to evaluate the relationship of these genes within the plant species. Based on the phylogenetic analysis results, TIPs were classified into five distinct arbitrary groups (group I to group V), which represented TIP2, TIP5, TIP4, TIP1, and TIP3, respectively. Group I represented the largest arbitrary group, followed by group IV, in the phylogenetic tree. The result clearly indicates that TIP2 and TIP1 are abundant aquaporins and highly related among the species. In the present review, a comparative study of gene structure analysis between dicots and monocots has been performed to analyze their structural variation. Most of the predicted motifs are conserved among the species, signifying an evolutionary relationship. The gene expression analysis indicated that the expression of TIP genes varies during different developmental stages and also during stressed conditions. The results indicated a great degree of evolutionary relationship and variation in the expression levels of TIPs in plants.

Design of inhibitors of the HIV-1 integrase core domain using virtual screening.

Acquired immunodeficiency syndrome (AIDS) is a disease of the human immune system caused by the human immunodeficiency virus (HIV). The integrase (IN) enzyme of HIV interacts with several cellular and viral proteins during the integration process. Thus, it represents an appropriate target for antiretroviral drugs (ARVs). We performed virtual screening of database compounds and designed analogues using Elvitegravir (EVG) as a standard compound. The 378 screened compounds were retrieved from ZINC, ChemSpider, PubChem, and ChemBank Chemical Databases based on chemical similarity and literature searches related to the structure of EVG. The Physiochemical properties, Bioactivity, Toxicity and Absorption, Distribution, Metabolism and Excretion of Molecules (ADME) of these compounds were predicted and docking Experiments were conducted using Molegro Virtual Docker software. The docking and ADME suggested very significant results in regard to EVG. The MolDock and Rerank scores were used to analyze the results. The compounds ZINC26507991 (-84.22), Analogue 9 (-68.49), ZINC20731658 (-66.79), ZINC00210363 (-43.44) showed better binding orientation with IN receptor model with respect to EVG (182.52). The ZINC26507991 has showed significant ADME result.