Tushar Khare

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants.

The microRNAs (miRNAs) are small (20–24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.

Individual and additive effects of Na+ and Cl− ions on rice under salinity stress

This study was attempted to assess the extent of toxicity contributed by Na+ and/or Cl− ions individually, besides their possible additive effects under NaCl using physiological and biochemical parameters. Despite the fact that most annual plants accumulate both Na+ and Cl− under saline conditions and each ion deserves equal considerations, most research has been focused on Na+ toxicity. Consequently, Cl− toxicity mechanisms including its accumulation/exclusion in plants are poorly understood. To address these issues, effects of equimolar (100 mM) concentrations of Na+, Cl− and NaCl (EC ≈ 10 dS m−1) were studied on 15-day-old seedlings of two rice cultivars, Panvel-3 (tolerant) and Sahyadri-3 (sensitive), using in vitro cultures. All three treatments induced substantial reductions in germination rate and plant growth with greater impacts under NaCl than Na+ and Cl− separately. Apparently, salt tolerance of Panvel-3 was due to its ability to exclude Na+ and Cl− from its shoots and maintaining low (<1.0) Na+/K+ ratios. Panvel-3 exhibited better vigour and membrane stability indices coupled with lower reactive oxygen species and lipid peroxidation levels, besides stimulated synthesis of proline, glycine betaine and ascorbic acid. Overall, the magnitude of toxicity was observed in NaCl > Na+ > Cl− manner. Though Cl− was relatively less toxic than its countercation, its effect cannot be totally diminished.

ROS-Induced Signaling and Gene Expression in Crops Under Salinity Stress

Salinity is one of the most serious environmental factors limiting the global productivity and superior quality of the agricultural crops, thus jeopardizing the capability of agronomic production to withstand the ever-increasing human population. Hypersaline conditions show multiple effects on crops such as water stress, ionic imbalance and toxicity, nutrition deficiency, oxidative stress, metabolic alterations, osmotic stress, and genotoxicity, which collectively reduce growth, development, and survival rate of the stressed crops. As a consequence, declined photosynthetic electron transport takes place, leading to the generation of reactive oxygen species (ROS) such as singlet oxygen, superoxide radical, hydrogen peroxide, and hydroxyl radical, albeit various forms and in different cellular compartments. These ROS are considered as key components for oxidative injury to lipid membrane and other vital cellular macromolecules, including nucleic acids, pigments, and proteins, eventually provoking cell death. To counteract the deleterious effects, these stress-induced ROS need to be scavenged by antioxidant machinery activated by the cells. Reports have advocated the ROS influenced expression of number of genes and signal transduction pathways, which implies the cellular strategies to use ROS as stimuli and signals that trigger and regulate numerous stress-responsive genetic networks. Therefore, in contrast to their acknowledged role as destructive species, ROS also act as signaling molecules in the regulation of salinity-induced alterations. The present chapter focuses on the role of ROS as signaling molecules and inducers of gene expression under the influence of saline conditions. We discuss herein the process of salinity-induced ROS generation, types of ROS, cellular damage by ROS, role of ROS as signaling molecules, and recent evidences of differential expression of antioxidants under saline conditions.

Engineering Crops for the Future: A Phosphoproteomics Approach

Abiotic stresses like salinity, drought, heat, metal ions, radiation and oxidative stress, and especially their combinations, are major limiting factors for growth and productivity of the crops. Various molecular and biochemical processes governing the plant responses to abiotic stresses have often been investigated and hold the key for producing high-yielding and abiotic stress-tolerant crops. Plant responses to abiotic stresses are dynamic and intricate, and vary with type, level, and duration of the stress involved, as well as on the type of tissue under stress. However, one biochemical indicator common to all stresses is definite and controlled protein phosphorylation which is generally transmitted by highly complex protein kinase cascades. In recent years, using different biochemical as well as computational tools, many of such phosphoproteins are identified and characterized with respect to abiotic stresses. Subsequently, an upsurge has been witnessed in recent times for phosphoproteomics repositories or databases. The use of this crucial knowledge about such proteins and their phosphorylation sites is one of the promising ways for crop engineering against abiotic stress. Several reports have described abiotic stress-induced transcriptome, proteome and phosphoproteome changes in plants subjected to these stress factors. However, the investigations to assess precise phosphoproteomics deviations in response to environmental stresses and their implementation for crop improvement are limited. The present review summarizes and discusses the recent developments in deciphering abiotic stress induced changes in plant phosphoproteome besides development of phosphoproteomics tools and their repositories. A critical assessment of targeting phosphoproteins for crop improvement and phosphoproteomics mediated enhanced abiotic stress tolerance in transgenic plants has been presented.

Engineering Phytohormones for Abiotic Stress Tolerance in Crop Plants

Abiotic stresses including salinity, drought, extreme temperatures, and heavy metals are posing serious threats to agricultural yields as well as the quality of produce. This necessitates the production of cultivars capable to withstand the harsh environmental conditions without substantial yield losses. Owing to the complexity underlying stress tolerance traits, conventional breeding techniques have met with limited success and demand effective supplements to feed the growing food demands worldwide. This necessitates the development and deployment of novel and potent approaches, and engineering of phytohormone metabolism could be a method of choice to produce climate resilient crops with higher yields. Phytohormones are considered critical for regulating and coordinating plant growth and development; however, in recent years, they have received great attention for their multifunctional roles in plant responses to environmental stimuli. Creditable research has shown that phytohormones including the classical ones – auxins, cytokinins, ethylene, gibberellins, and newer members including brassinosteroids, jasmonates, and strigolactones – may prove to be potent targets for their metabolic engineering for producing abiotic stress-tolerant crop plants. This chapter presents short description of the roles of phytohormones in abiotic stress responses and tolerance followed by reviewing attempts made by the plant biotechnologists for engineering of phytohormone metabolism, signal, transport, and perception to develop abiotic stress-tolerant crop plants.

RNAi Technology: The Role in Development of Abiotic Stress-Tolerant Crops

Abstract Over the past two decades, genetic engineering and related techniques have demonstrated striking progress in manipulation of the genes for induction of the desired characteristics into transgenic organisms. The regulatory mechanism of RNA interference (RNAi) has been studied in many higher organisms. The accuracy and precision of this phenomenon assures a great success rate in plant improvement. The RNAi provides us with an explicit methodology for down-regulation of genes of interest without hampering the expression of any other gene in the plant. The examination of different RNAi pathways, along with their components, including microRNAs and small interfering RNAs, have provided us with more than one way to achieve gene manipulation for mediated crop improvement. The phenomenon of RNAi has been studied in different abiotic environments; such as salinity, drought, extreme temperatures, heavy metals, and nutrition deprivation and radiation in various crops. RNAi-mediated crop manipulations have been reported that incorporate the utilization of vital stress-responsive elements with their subsequent mRNA and/or protein targets. Hence, collectively, RNAi technology has proven to be a promising tool for abiotic stress improvement in crops. This chapter focuses on the potential and successful application of RNAi technology for crop improvement in response to various abiotic stress factors.

Exploring miRNAs for developing climate-resilient crops: A perspective review

Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.

Systems Biology Approach for Elucidation of Plant Responses to Salinity Stress

Salinity is one of the most detrimental abiotic stress factors responsible for qualitative and quantitative deterioration in global crop production. By considering the inclusive food requirements, deciphering the complex salinity-mediated responses in plants is significant to develop salt-tolerant crops with higher yields. The recent advancements in analytical technologies have made possible to investigate and generate huge amount of data. Various tools have been successfully employed to check salt-induced alterations at genome, transcriptome, proteome, and metabolome levels of plants. Omics tools in combination with computational biological analysis have provided important information, which can be used to generate biological databases as well as in silico tools. Hence this combinatorial approach of omics-systems biology is currently considered as ultimate path in plant stress physiology analysis, which aims to improve agronomic characters. The present chapter is therefore focused on omics-mediated systems biology-based investigations targeting salinity responses in plants. This chapter also highlights precise computational tools and databases to analyze transcription factors, quantitative trait loci, and small RNAs. Collectively, the chapter illustrates the system biology approach as an essential and convenient tool in salinity studies.

Polyamines and Their Metabolic Engineering for Plant Salinity Stress Tolerance

Polyamines (PAs) are small polycationic aliphatic amines and are ubiquitous in the plant kingdom. They play important roles in plant growth, development, and stress responses. Several research reports have established a correlation between their accumulation and salt stress tolerance in different plant species. Creditable research in the recent past has proved their vital roles in stress responses and adaptation strategies employed by plants, including scavenging of free radicals, neutralization of acids, and stabilization of cell membranes. They are able to bind several charged molecules including DNA, proteins, membrane phospholipids, and pectic polysaccharides, and have been credited with roles in protein phosphorylation and post-transcriptional modifications. They also play important roles in plant growth regulation, as well as acting as signaling molecules. Owing to their diverse functions in plant growth, development, and stress responses, they have emerged as potent targets for metabolic engineering to confer salt stress tolerance on manipulated plants. This chapter highlights their biosynthesis and transport, their exogenous applications to alleviate salt stress, and their metabolic engineering for developing salt-tolerant plants.

Impact of Nanoparticles on Oxidative Stress and Responsive Antioxidative Defense in Plants

Abstract Nanotechnology has emerged as a multidisciplinary field with a wide range of potential applications including agriculture, where nanoparticles (NPs) are making a mark in improving the efficiency of fertilizers and pesticides. Though the main aim of usage of NPs is enhanced crop growth and yield improvements, contemporary reports have indicated both positive as well as negative impacts of NPs on plants. Certain reports have postulated that NPs can induce phytotoxicity and have negative impacts on overall plant metabolism, but simultaneously the exclusive properties of NPs can be used to improve crop performance as well. Nevertheless, unspecified release of NPs into the ecosystem has raised global concern about their potential phytotoxic effects, which needs to be fixed for commercial and large-scale use of NPs for the betterment of crop production. One of the prime detrimental effects of NP release in the environment is induction of oxidative stress, which is a complex physiological, biochemical, and molecular phenomenon that accompanies virtually all biotic and abiotic stresses in higher plants and develops as a result of overproduction and accumulation of reactive oxygen species (ROS). Engineered NPs, whether carbon or metal based, have been reported to impart oxidative stress and ROS generation in many plants. In this chapter we discuss the oxidative stress induced by different NPs in plants as well as responsive antioxidant machinery including enzymatic and nonenzymatic antioxidative components in stressed plants.