The Role of Long Noncoding RNAs in Plant Stress Tolerance

Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits

MAIN CONCLUSION

Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.

Genome-wide identification and characterization of long non-coding RNA in barley roots in response to Piriformospora indica colonization

Currently, there is very limited information about long noncoding RNAs (lncRNAs) found in barley. It remains unclear whether barley lncRNAs are responsive to Piriformospora indica (P. indica) colonization.We found that barley roots exhibited fast development and that large roots branched after P. indica colonization. Genome-wide high-throughput RNA-seq and bioinformatic analysis showed that 4356 and 5154 differentially expressed LncRNAs (DELs) were found in response to P. indica at 3 and 7 days after colonization (dai), respectively, and 2456 DELs were found at 7 dai compared to 3 dai. Based on the coexpression correlation of lncRNAmRNA, we found that 98.6% of lncRNAs were positively correlated with 3430 mRNAs at 3 dai and 7 dai. Further GO analysis showed that 30 lncRNAs might be involved in the regulation of gene transcription; 23 lncRNAs might participate in cell cycle regulation. Moreover, the metabolite analysis indicated that chlorophyll a, sucrose, protein, gibberellin, and auxin were in accordance with the results of the transcriptome, and the respective lncRNAs were positively correlated with these target RNAs. Gene silencing suggested that lncRNA TCONS_00262342 is probably a key regulator of GA₃ synthesis pathway, which participates in P. indica and barley interactions. We concluded that acting as a molecular material basis and resource, lncRNAs respond to P. indica colonization by regulating metabolite content in barley and coordinate the complex regulatory process of higher life by constructing highly positive correlations with their target mRNAs.

LncRNA PMAT-PtoMYB46 module represses PtoMATE and PtoARF2 promoting Pb2+ uptake and plant growth in poplar

Lead (Pb²⁺) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb²⁺ uptake in woody plants remains unclear. Here, we identified 226 Pb²⁺-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb²⁺-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb²⁺ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT-PtoMYB46-PtoMATE-PtoARF2 regulatory module control Pb²⁺ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb²⁺ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.

Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation

Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.

Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage

Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01059-2.

The hypoxia-reoxygenation stress in plants

Plants are very plastic in adapting growth and development to changing adverse environmental conditions. This feature will be essential for plants to survive climate changes characterized by extreme temperatures and rainfall. Although plants require molecular oxygen (O2) to live, they can overcome transient low-O2 conditions (hypoxia) until return to standard 21% O2 atmospheric conditions (normoxia). After heavy rainfall, submerged plants in flooded lands undergo transient hypoxia until water recedes and normoxia is recovered. The accumulated information on the physiological and molecular events occurring during the hypoxia phase contrasts with the limited knowledge on the reoxygenation process after hypoxia, which has often been overlooked in many studies in plants. Phenotypic alterations during recovery are due to potentiated oxidative stress generated by simultaneous reoxygenation and reillumination leading to cell damage. Besides processes such as N-degron proteolytic pathway-mediated O2 sensing, or mitochondria-driven metabolic alterations, other molecular events controlling gene expression have been recently proposed as key regulators of hypoxia and reoxygenation. RNA regulatory functions, chromatin remodeling, protein synthesis, and post-translational modifications must all be studied in depth in the coming years to improve our knowledge on hypoxia-reoxygenation transition in plants, a topic with relevance in agricultural biotechnology in the context of global climate change.

Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley

Environmental stresses such as salinity, drought, heat, freezing, heavy metal and even pathogen infections seriously threaten the growth and yield of important cereal crops including wheat and barley. There is growing evidence indicating that plants employ sophisticated epigenetic mechanisms to fine-tune their responses to environmental stresses. Here, we provide an overview of recent developments in understanding the epigenetic processes and elements—such as DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs—involved in plant responses to abiotic and biotic stresses in wheat and barley. Potentials of exploiting epigenetic variation for the improvement of wheat and barley are discussed.

Lysine, Lysine-Rich, Serine, and Serine-Rich Proteins: Link Between Metabolism, Development, and Abiotic Stress Tolerance and the Role of ncRNAs in Their Regulation

Lysine (Lys) is indispensable nutritionally, and its levels in plants are modulated by both transcriptional and post-transcriptional control during plant ontogeny. Animal glutamate receptor homologs have been detected in plants, which may participate in several plant processes through the Lys catabolic products. Interestingly, a connection between Lys and serotonin metabolism has been established recently in rice. 2-Aminoadipate, a catabolic product of Lys appears to play a critical role between serotonin accumulation and the color of rice endosperm/grain. It has also been shown that expression of some lysine-methylated proteins and genes encoding lysine-methyltransferases (KMTs) are regulated by cadmium even as it is known that Lys biosynthesis and its degradation are modulated by novel mechanisms. Three complex pathways co-exist in plants for serine (Ser) biosynthesis, and the relative preponderance of each pathway in relation to plant development or abiotic stress tolerance are being unfolded slowly. But the phosphorylated pathway of L-Ser biosynthesis (PPSB) appears to play critical roles and is essential in plant metabolism and development. Ser, which participates indirectly in purine and pyrimidine biosynthesis and plays a pivotal role in plant metabolism and signaling. Also, L-Ser has been implicated in plant responses to both biotic and abiotic stresses. A large body of information implicates Lys-rich and serine/arginine-rich (SR) proteins in a very wide array of abiotic stresses. Interestingly, a link exists between Lys-rich K-segment and stress tolerance levels. It is of interest to note that abiotic stresses largely influence the expression patterns of SR proteins and also the alternative splicing (AS) patterns. We have checked if any lncRNAs form a cohort of differentially expressed genes from the publicly available PPSB, sequence read archives of NCBI GenBank. Finally, we discuss the link between Lys and Ser synthesis, catabolism, Lys-proteins, and SR proteins during plant development and their myriad roles in response to abiotic stresses.

Beneficial Effects of Salt on Halophyte Growth: Morphology, Cells, and Genes

Halophytes can survive and complete their life cycle in the presence of ≥200 mM NaCl. These remarkable plants have developed various strategies to tolerate salinity and thrive in high-salt environments. At the appropriate levels, salt has a beneficial effect on the vegetative growth of halophytes but inhibits the growth of non-halophytes. In recent years, many studies have focused on elucidating the salt-tolerance mechanisms of halophytes at the molecular, physiological, and individual level. In this review, we focus on the mechanisms, from the macroscopic to the molecular, underlying the successful growth of halophytes in saline environments to explain why salt has beneficial effects on halophytes but harmful effects on non-halophytes. These mechanisms include the specialized organs of halophytes (for example, ion compartmentalization in succulent leaves), their unique structures (salt glands and hydrophobic barriers in roots), and their salt-tolerance genes. We hope to shed light on the use of halophytes for engineering salt-tolerant crops, soil conservation, and the protection of freshwater resources in the near future.