Salt stress induced ion accumulation, ion homeostasis, membrane injury and sugar contents in salt-sensitive rice (Oryza sativa L. spp. indica) roots under isoosmotic conditions

Excess salt induced ionic and osmotic stresses that disturbed metabolism and led to reduction of plant development. Previous studies reported that sugars in stressed plants were involved in stress tolerance. However, the role of sugars in salt-stressed plants against only ionic effects is still unclear. The objective of this research was to investigate accumulation and homeostasis of ions, membrane injury, water content, growth characters and sugar contents in roots, in-response to salt stress under iso-osmotic conditions. Salt-sensitive rice, Pathumthani1 (PT1) was grown on MS culture medium for 7 days and was adjusted to salt stress under iso-osmotic conditions (-1.75 ± 0.20 MPa) by mannitol for 4 days. An increase in NaCl increased Na+ and Na+:K+ in PT1 roots leading to increased membrane injury, while the water content was decreased. Additionally, growth characters, including number, length, fresh weight and dry weight of roots, were inhibited. Sugar accumulations in PT1 roots were enhanced by increases in NaCl. The increase in Na+ was positively related to total soluble sugars, resulting in an osmotic adjustment of the membrane that maintained water availability. The accumulation of sugars in PT1 roots may be a primary salt-defense mechanism and may function as an osmotic control.Key words: Mannitol, membrane injury, oligosaccharides, sodium ion, potassium ion, sodium chloride

Ribosome profiling reveals the what, when, where and how of protein synthesis

Ribosome profiling, which involves the deep sequencing of ribosome-protected mRNA fragments, is a powerful tool for globally monitoring translation in vivo. The method has facilitated discovery of the regulation of gene expression underlying diverse and complex biological processes, of important aspects of the mechanism of protein synthesis, and even of new proteins, by providing a systematic approach for experimental annotation of coding regions. Here, we introduce the methodology of ribosome profiling and discuss examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products

Impact of uORFs in mediating regulation of translation in stress conditions

Background: A large fraction of genes contains upstream ORFs (uORFs) in the 5' untranslated region (5'UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question. Results: By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe. Conclusion: We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches.1. Ministerio de Ciencia e Innovación (MCI), Agencia Estatal de Investigación (AEI) grants BFU2015–65235-P and PGC2018–094091-B-I00, co-funded by Fondo Europeo de Desarrollo Regional (FEDER); 2. Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya, grant 2017SGR01020; 3. Spanish National Bioinformatics Institute (INB), funded by ISCIII and FEDER, grant PT17/0009/0014 of the PE I + D + i 2013–2016