Regulatory short RNAs: A decade's tale for manipulating salt tolerance in plants

Abstract

Salt stress is a globally increasing environmental detriment to crop growth and productivity. Exposure to salt stress evokes a complex medley of cellular signals, which rapidly reprogram transcriptional and metabolic networks to shape plant phenotype. To date, genetic engineering approaches were used with success to enhance salt tolerance; however, their performance is yet to be evaluated under realistic field conditions. Regulatory short non‐coding RNAs (rsRNAs) are emerging as next‐generation candidates for engineering salt tolerance in crops. In view of this, the present review provides a comprehensive analysis of a decade's worth of functional studies on non‐coding RNAs involved in salt tolerance. Further, we have integrated this knowledge of rsRNA‐mediated regulation with the current paradigm of salt tolerance to highlight two regulatory complexes (RCs) for regulating salt tolerance in plants. Finally, a knowledge‐driven roadmap is proposed to judiciously utilize RC component(s) for enhancing salt tolerance in crops.

Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa

“…These non-coding RNAs mainly include small non-coding RNA (sncRNA) and long non-coding (LncRNA). miRNA is one of the major parts of sncRNAs, as well as the siRNA; and they mediate gene silencing and hence regulate the expression levels of the genes ( Negi et al, 2021 ). Mul-miR3954, for example, was discovered in Arabidopsis to improve the salt-tolerance level of transgenic plants ( Gai et al, 2018 ); miR398b and miR298 could regulate Cu/Zn- SOD expression in response to ROS levels induced by salt stress ( Feng et al, 2010 ).…”

miRNAomic Approach to Plant Nitrogen Starvation

“…The miRISC uncapped and sensitive 3′ cleavage products are degraded by the exonucleases (EXONUCLEASE4 being identified while the other nucleases were still unknown). On the other hand, capped 5′ cleavage products first undergo uridylation by HESO1 [ 32 ] and are then cleaved by RISC-INTERACTING CLEARING 3′-5′ EXORIBONULEASE 1 (RICE1) and (RICE2) [ 33 ] assisted by some RNA exosome cofactors including SKI2, SKI3, and SKI8 [ 34 ] Repression at the translational level: In addition to target messenger RNA cleavage, miRNAs negatively regulate the gene expression through translational repression also [ 35 ]. In the case of plants, although miRNAs and their target mRNAs have mostly near-perfect complementarity in their sequences, nevertheless, the negative regulation via translational repression is extensive [ 36 ].…”

“…The miRISC uncapped and sensitive 3′ cleavage products are degraded by the exonucleases (EXONUCLEASE4 being identified while the other nucleases were still unknown). On the other hand, capped 5′ cleavage products first undergo uridylation by HESO1 [ 32 ] and are then cleaved by RISC-INTERACTING CLEARING 3′-5′ EXORIBONULEASE 1 (RICE1) and (RICE2) [ 33 ] assisted by some RNA exosome cofactors including SKI2, SKI3, and SKI8 [ 34 ]…”

“…Numerous studies have demonstrated the changes in the expression level of different miRNA families in N limitation conditions in various plant species such as Arabidopsis [ 51 , 52 ], maize [ 53 , 54 ], sorghum [ 55 ], rice [ 32 ], and soybean [ 33 ]. The altered expression pattern of these miRNAs has been shown to play crucial roles in plant adaptive responses to N limitation via the mediation of the expression of their target genes involved in N uptake and remobilization [ 56 ].…”

Transcriptional and post‐transcriptional mechanisms regulating salt tolerance in plants

“…They are generally associated with TF-binding sites and epi(genomic)/chromatin features, and they can be explored as potent targets for engineering salinity stress tolerance in plants. Negi et al (2021) reviewed the regulatory short RNAs and important developments in recent years toward their use for manipulating salt tolerance in plants. Singh and Roychoudhury (2021) presented important insights into the gene regulation at transcriptional and post-transcriptional levels, including microRNA-mediated regulation, genome editing and alternative splicing, to combat salt stress in plants.…”