Translational response of salt-tolerant rice plants

Vaishnavi Kardale, Bioinformatics Centre, Savitribai Phule Pune University

Rice is one of the most popular staple crops with about half of the world population consuming it every day. Rice unfortunately is sensitive to salt especially the seedling and reproductive stage as compared to other developmental stages. Global rice production is threatened due to reduced yield and substandard quality as a result of increased soil salinization. Better knowledge of salt tolerance in rice is essential for engineering plants with improved salt tolerance to feed an increasing global population.

What is salt stress?

The excess amount of Na+ and Cl- in soil inhibits plant growth by Na+ toxicity and osmotic stress. Some plants have evolved acclimation mechanisms to survive under salt stress, such as salt overly sensitive (SOS) pathway and reactive oxygen species (ROS) scavenging system. Several genes have been identified that contribute to salt tolerance in rice, maize, and tomato but they have not been successfully cloned.

With the development of high-throughput methodologies such as NGS and mass spectrometry genome analysis, transcriptomics and proteomics have become more feasible. However, gene expression is regulated not just at transcriptional but also at translation level via microRNA and ribosome stalling. It is increasingly evident that transcriptomic and translational responses are independent of one another and thus translational responses must also be thoroughly investigated.

A recent study conducted:

In recent research published in BMC Genomics, researchers performed RNA-seq and ribo-seq with the seedling shoot of salt-sensitive rice ‘Nipponbare’ (NB) and salt-tolerant ‘Sea Rice 86’ (SR86) under normal and stress conditions. To perform ribo-seq, polysomes were digested with ribonucleases to obtain the ribosome-protected mRNA fragment (RPF) to construct a library. Having sequenced the RPF and RNA library, data analysis can reveal information about in-vivo translation.

Important findings of the study:

Yang et al. found inconsistency in the transcriptomic and translational responses to salt stress in each cultivar. This suggests that translational regulation represents an independent salt stress response. Both NB and SR86 adopted different translational regulation pathways to adapt to salt stress. The researchers also observed a stronger translational response in Sea Rice 86 (SR86). Ribosome occupancy along the coding region was found to be biased. This bias increased during salt stress, particularly in SR86.

This suggests that more dynamic ribosomes are present in salt-tolerant cultivars. Under salt stress, translation inhibitory processes like ribosome stalling were accelerated in NB but decreased in SR86. This finding is another example of the divergent ribosome dynamics between NB and SR86. These findings show the translational response of rice under salt stress. Potential targets for genetic manipulation can thus be identified so that rice plants with increased salt tolerance can be developed.

Also read: White-tailed deer in Michigan found to contain Covid antibodies!

Reference:

1. Yang, X., Song, B., Cui, J. et al. Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice. BMC Genomics 22, 612 (2021). https://doi.org/10.1186/s12864-021-07922-6

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Author info:

Vaishnavi Kardale is a master’s student at the Bioinformatics Centre, Savitribai Phule University. She is interested in protein folding mechanisms and wants to study them further.

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