Nitric oxide, energy and redox-dependent responses to hypoxia.

Hypoxia occurs when the oxygen levels fall below the levels required for mitochondria to support respiration. Regulated hypoxia is associated with quiescence, particularly in storage organs (seeds) and stem cell niches. In contrast, environmentally-induced hypoxia poses significant challenges for metabolically-active cells that are adapted to aerobic respiration. The perception of oxygen availability through cysteine oxidases, which function as oxygen-sensing enzymes in plants that control the N-degron pathway, and the regulation of hypoxia-responsive genes and processes is essential to survival. Functioning together with reactive oxygen species (ROS), particularly hydrogen peroxide and reactive nitrogen species (RNS), such as nitric oxide (•NO), nitrogen dioxide (•NO2), S-nitrosothiols (SNOs), and peroxynitrite (ONOO-), hypoxia signaling pathways trigger anatomical adaptations such as formation of aerenchyma, mobilization of sugar reserves for anaerobic germination, formation of aerial adventitious roots and hyponastic response. NO and hydrogen peroxide (H2O2) participate in local and systemic signaling pathways that facilitate acclimation to changing energetic requirements, controlling glycolytic fermentation, the GABA shunt and amino acid synthesis. NO enhances antioxidant capacity and contributes to the recycling of redox equivalents energy metabolism through the phytoglobin (Pgb)-NO cycle. Here, we summarize current knowledge, highlighting the central role of NO and redox regulation in adaptive responses that prevent hypoxia-induced death in challenging conditions such as flooding.

Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.).

A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1-2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant's growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene's expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant's growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.

Computational Modelling, Functional Characterization and Molecular Docking to Lead Compounds of Bordetella pertussis Diaminopimelate Epimerase.

Bordetella pertussis, the causative agent of whooping cough, is an opportunistic virulent bacterial pathogen that is resistant to a wide range of antibiotics due to a variety of resistance mechanisms. Looking at the increasing number of infections caused by B. pertussis and its resistance to diverse antibiotics, it is essential to develop alternative strategies to fight against B. pertussis. Diaminopimelate epimerase (DapF) is an important enzyme of the lysine biosynthesis pathway in B. pertussis that catalyzes the formation of meso-2, 6-diaminoheptanedioate (meso-DAP), which is an important step in lysine metabolism. Therefore, Bordetella pertussis diaminopimelate epimerase (DapF) becomes an ideal target for antimicrobial drug development. In the present study, computational modelling, functional characterization, binding studies, and docking studies of BpDapF with lead compounds were carried out using different in silico tools. In silico prediction results in the secondary structure, 3-D structure analysis, and protein-protein interaction analysis of BpDapF. Docking studies further showed the respective amino acid residues for ligands in the phosphate­binding loop of BpDapF play a vital role in the formation of H­bonds with these ligands. The site where the ligand was bound is a deep groove, which is regarded as the binding cavity of the protein. Biochemical studies indicated that Limonin (binding energy - 8.8 kcal/mol), Ajmalicine (binding energy - 8.7 kcal/mol), Clinafloxacin (binding energy - 8.3 kcal/mol), Dexamethasone (binding energy - 8.2 kcal/mol), and Tetracycline (binding energy - 8.1 kcal/mol) exhibited promising binding towards the drug target DapF of B. pertussis in comparison with the binding between other drugs and act as the potential inhibitors of BpDapF that eventually can reduce the catalytic activity of BpDapF.

Abiotic stress tolerance in plants: a fascinating action of defense mechanisms.

Climate fluctuation mediated abiotic stress consequences loss in crop yields. These stresses have a negative impact on plant growth and development by causing physiological and molecular changes. In this review, we have attempted to outline recent studies (5 years) associated with abiotic stress resistance in plants. We investigated the various factors that contribute to coping with abiotic challenges, such as transcription factors (TFs), microRNAs (miRNAs), epigenetic changes, chemical priming, transgenic breeding, autophagy, and non-coding RNAs. Stress responsive genes are regulated mostly by TFs, and these can be used to enhance stress resistance in plants. Plants express some miRNA during stress imposition that act on stress-related target genes to help them survive. Epigenetic alterations govern gene expression and facilitate stress tolerance. Chemical priming enhances growth in plants by modulating physiological parameters. Transgenic breeding enables identification of genes involved in precise plant responses during stressful situations. In addition to protein coding genes, non-coding RNAs also influence the growth of the plant by causing alterations at gene expression levels. For achieving sustainable agriculture for a rising world population, it is crucial to develop abiotic-resistant crops with anticipated agronomical traits. To achieve this objective, understanding the diverse mechanisms by which plants protect themselves against abiotic stresses is imperative. This review emphasizes on recent progress and future prospects for abiotic stress tolerance and productivity in plants.

Nitric oxide mediated alleviation of abiotic challenges in plants.

Agriculture and ecosystem are negatively influenced by the abiotic stresses which create solemn pressures on plants as they are sessile in nature leading to excessive losses in economy. For maintenance of sustainable agriculture and to fulfil the cumulative call of food for rapidly growing population worldwide, it becomes crucial to protects the crop plants from climate fluctuations. Plants fight back against these challenges by generation of redox molecules comprising reactive oxygen species (ROS) and reactive nitrogen species (RNS) and cause modulation at cellular, physiological and molecular levels. Nitric oxide (NO) deliver tolerance to several biotic and abiotic stresses in plants by acting as signalling molecule or free radicals. It is also intricated in several developmental processes in plants using different mechanisms. Supplementation of exogenous NO reduce toxicity of abiotic stresses and provide resistance. In this review article, we summarize the recent research studies (five years) depicting the functional role of NO in alleviation of abiotic stresses such as drought, cold, heat, heavy metals and flooding. Moreover, by investigating studies found that among heavy metals works associated with Hg, Pb, and Cr is limited comparatively. Additionally, role of NO in abiotic stress resistance such as cold, freezing and heat stress less/poorly investigated. Consequently, further emphasis should be diverted towards how NO can facilitate protection against these stresses. In recent studies mostly beneficial role of NO against abiotic challenges have been elucidated by observing physiological/biochemical parameters but relatively inadequate research done at the transcripts level or gene regulation subsequently researchers should include it in future. Lastly, brief outline and an evaluative discussion on the present information and future prospective provided. Altogether, these inclusive experimental agendas could facilitate in future to produce climate tolerant plants. This will help to confront the constant fluctuations in the environment and to reduce the challenges in way of agriculture productivity and global food demands.

Protective role of nitric oxide on nitrogen-thiol metabolism and amino acids profiling during arsenic exposure in Oryza sativa L.

Nitric oxide (NO) being a signaling molecule inside the plant cells, play significant role in signaling cascades and protection against environmental stresses. However, the protective role of NO in alleviating As toxicity in rice plants is currently not available. In the present study, the level of NO, nitrogen (N), inorganic N (nitrate, ammonium), thiols {TT (Total thiols), NPT (Nonprotein thiol)} and AAs contents along with N assimilating enzymes (NR, GDH, GOGAT) were analyzed after exposure of AsIII/NO treatment alone, and in combination. NO supplementation enhanced the content of N, inorganic N & thiol contents, NR, GOGAT activities, when compared with AsIII exposure alone. In AsIII exposed rice seedlings, content of AAs (except His, Arg, Met) reduced over the control, while supplementation of SNP improved AAs contents, compared to AsIII treatment alone. In conclusion, rice seedlings supplemented with NO tolerate the AsIII toxicity by reducing the N related parameters, thiol contents, altering the AA profile and enhanced the nutritional quality by increasing EAAs (essential amino acids) and NEAAs (non-essential amino acids).

Sulphur potentiates selenium to alleviate arsenic-induced stress by modulating oxidative stress, accumulation and thiol-ascorbate metabolism in Brassica juncea L.

The present study was designed to see the influence of selenium (Se) and sulphur (S) in the alleviation of arsenic (As)-induced stress in Brassica juncea plant. Se-induced alterations in physiological and biochemical responses due to deficient S (DS), normal S (NS) and additional S (AS) conditions were evaluated in 14-day-old seedlings of B. juncea variety Varuna. During the last 7 days of the 14-day-old seedlings, supplementation with arsenite (AsIII, 300 µM) alone and its combination with selenite (SeIV, 50 µM) along with different S treatments was done which are as follows: (i) control; (ii) As; (iii) As+Se+DS; (iv) As+Se + NS; (v) As+Se + AS. Experimental results showed that the application of AS in spite of NS supplied with Se influenced plant growth, oxidative stress and thiol-ascorbate-related parameters more prominently under As stress. The plants with As+Se+AS treatment exhibited lower ROS (superoxide and hydrogen peroxide ion), malondialdehyde (MDA) accumulation and lipoxygenase activity with increased activities of superoxide dismutase, catalase and ascorbate peroxidase compared with As+Se+NS condition. These plants also exhibited an increase in cysteine, non-protein thiols and phytochelatins, along with reduced, oxidised and redox content of glutathione and ascorbate. Furthermore, the application of S along with Se increased the activities of glutathione reductase, glutathione S-transferase, glutathione peroxidase, monodehydroascorbate and dehydroascorbate to minimise As stress. However, we observed that these responses were reversed under As+Se+DS condition and induced oxidative stress, which was almost similar to As only treatment. It indicated that AS nutrition potentiated Se to alleviate As-inhibited plant growth by modulating antioxidants including thiol-ascorbate-based mechanism and reducing As accumulation in B. juncea plants.

Nitric oxide alters nitrogen metabolism and PIN gene expressions by playing protective role in arsenic challenged Brassica juncea L.

Plants have ability to adapt themselves through altering their growth process. In the present study, we examined exogenous application of nitric oxide (NO) on nitrogen metabolism and auxin (PIN) gene expression, and its possible role in alleviation of arsenic (As) toxicity in Brassica juncea seedlings. Seven days old hydroponically grown B. juncea seedlings were exposed to AsIII (150 µM), Sodium nitroprusside (NO donor, 100 µM), AsIII + SNP and control (without metal)for 48 h. Experimental results revealed that AsIII stress: enhanced the level of nitrite, NiR activity, NO3- and NH4+content as well as NADH-GOGAT activity; but GDH level decreased; enhanced content of amino acids; upregulated gene expression level of N metabolism and downregulated polar auxin transporter genes (PIN); inhibited plant growth and morphological parameters; increased MDA, H2O2, cysteine, proline content, enzymatic antioxidants (SOD, CAT, APX; GSH, TT, NPT); and decreased nutrient content. AsIII + SNP combination reduced the accumulation of As; improved growth; chlorophyll, protein and mineral nutrient content by scavenging ROS generation; maintained amino acids content; downregulated expression of N metabolism genes and upregulated expression of auxin transporter (PIN) genes . Additional biochemical data depicts reduction in the level of nitrogen related enzymatic activities, and other stress related parameters. Overall, this study provides an integrated view that exogenous SNP (NO donor) supplementation alleviated the inhibitory role of AsIII in B. juncea seedlings by altering nutrients, amino acids and auxin redistribution via expression of nitrogen and PIN gene profiling.

Nitric oxide confronts arsenic stimulated oxidative stress and root architecture through distinct gene expression of auxin transporters, nutrient related genes and modulates biochemical responses in Oryza sativa L.

Plants have the ability to adapt themselves under stressed conditions through reprogramming their growth and development. Understanding the mechanisms regulating overall growth of stressed plant is an important issue for plant and environmental biology research. Although the role of NO in modulating arsenic (As) toxicity is known, nitric oxide (NO) induced alteration in auxin and nutrient related transporters during As stress in rice is poorly understood. Experimental results showed that As exposure decreased gene expression level of polar auxin transporter (PIN proteins), and nutrient transporter related genes (AMT, NRT, NiR, PHT, KTP). The improved tolerance induced by As + NO combination is attributed to reduced As accumulation in rice seedlings, improved root architectural changes, overall growth of plant, chlorophyll, protein content, and accumulation of mineral nutrients by reducing the ROS generation. Further, enhanced transcript levels of PIN proteins and mineral nutrition related genes were also observed under As + NO treatment. Additional biochemical data revealed enhanced oxidative stress by increasing the level of antioxidant enzymes, and stress-related parameters. Overall, the study provides an integrated view of plant response during As + NO interaction to change the plant metabolism through different cellular processes.