Insights on Plant Abiotic Stress Tolerance via Translatomics
Translation is a tightly controlled mechanism in response to abiotic stress tolerance in plants, partly due to how energetically expensive translation is. Under hostile conditions, plants significantly downregulate growth, choosing to conserve resources until more favourable conditions return. Translation also plays a key role in rapidly producing protective proteins, increasing the likelihood of survival. With the advent of climate change and more extreme weather events, understanding the mechanisms of the translational responses to these stimuli is all the more pertinent, and knowledge in this area may go a long way towards constructing genetically modified plant strains. Here, we delve into our pick of three relevant ribosome profiling papers in the area.
Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress
The Plant Journal, 2015; 84(6), pp1206-18
Lei, L., Shi, J., Chen, J., Zhang, M., Sun, S., Xie, S., Li, X., Zeng, B., Peng, L., Hauck, A. and Zhao, H.
Transcriptional regulation in response to stress in plants has been relatively well studied, utilising many RNA sequencing technologies. However, with the advent of ribosome profiling methodologies, an understanding of the translational regulation of the stress response is becoming more widespread. Of these stressors initiating stress response, drought is particularly pertinent, with the increasing likelihood of extreme weather events concurrent with climate change. In this paper, the authors examine the translational mechanisms employed in maize seedlings, under normal and drought conditions.
- Under drought conditions, there were a greater number of downregulated genes vs upregulated genes at both the transcriptional and translational level (approx. 1,700 upregulated genes, approx. 3,300 downregulated genes). Regarding the fold difference among altered genes, there was a moderate correlation between transcription and translation.
- Of the genes that were responsive to drought conditions, less than half of them were shared between transcription and translation, suggesting independent regulation of each level. Additionally, a large number of genes had significantly altered translational efficiencies (TE). Furthermore, there was significantly more downregulated genes at the translational level vs the transcriptional level.
- In coding sequences, certain features contributed to an increase in translational efficiency of the gene, including higher GC content, shorter lengths and lower normalised minimal free energy (NMFE). However, when analysing the 5’ untranslated region, a higher NMFE and lower GC content were more consistent with increased translational efficiency of the gene.
- The authors demonstrated the presence of upstream ORFs across ~8,000 genes within the maize genome. Translated uORFs had a number of common features, such as longer length and greater folding potential (as compared to untranslated uORFs).
- Genes with translated uORFs tended to have shorter 5’UTRs. These uORFs also have a shorter distance to the start codon of their main ORF as compared to untranslated uORFs. Furthermore, these features did not differ between genes that responded to drought stress and those that did not. Crucially, genes that expressed translated uORFs experienced significantly decrease TE in their main ORF.
This work has demonstrated varying strategies to drought conditions in maize, with independent regulation of transcription and translation being observed. Furthermore, the features uncovered to impact on translational efficiency could potentially be used as markers for genes with high likelihood of altered translational regulation. Additionally, it demonstrates the importance of uORFs in translational regulation.
Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq
BMC Plant Biology, 2016; 16(1), pp.1-13.BMC
Lukoszek, R., Feist, P. and Ignatova, Z.
The response to heat is a key process in the survival of plants, with plants reacting on a global scale through alteration of a wide range of systems. In order to initiate these changes, it has been demonstrated that plants significantly alter transcription, with many clusters of genes undergoing up- or down-regulation. While transcriptional regulation in plants due to thermal stress has been well studied, the level of research into translational regulation is comparatively understudied. Here, the authors investigate the alteration in translational regulation in response to heat stress in Arabidopsis thaliana.
- In general, there was a coordinated response across transcriptional and translational regulation, with there being correlating changes in genes altered between RNA-Seq and Ribo-Seq datasets, although there was a small subset of genes which differed independently in these datasets.
- Expectedly, genes involved in heat shock response and protein folding were upregulated, while genes involved in chromatic structure, cytoskeletal organisation, cell wall synthesis, and the cell cycle were downregulated.
- In genes translationally upregulated in response to heat, the folding energy of the mRNA upstream (100 bp) of the start codon of the mRNAs was significantly higher than those that were unaltered or downregulated.
- Within genes translationally upregulated under heat stress, a significant number had the presence of G3 quadruplexes in their coding sequence (CDS), and G2 quadruplexes in their 5’ untranslated region (UTR), CDS, and 3’ UTR. Ribosome protected fragment coverage was also higher in these G2 quadruplexes in the 5’ and 3’UTRs in the heat stress group. Additionally, the presence of G2 quadruplexes in the 5’ UTR correlated more strongly with downstream translational expression of the CDS in the heat stress group vs the control group.
- The authors uncovered an alternative transcript and ORF in the At1g76880 gene, with there being drastically more reads post the 2195nt mark under induction of heat stress. Furthermore, motifs were uncovered in the putative promotor region of this alternative transcript that share features with known heat shock promotor motifs.
While much of the results in this paper were largely expected, with an upregulation of genes relating to heat shock proteins at both the transcriptional and translational level, some novel insights were obtained. The folding energy of mRNAs appears to play a role in translational regulation specifically, and thus could perhaps be used as a marker for discovery of other genes related to this function in other species. This may partially be explained by the presence of G2 quadruplexes, which may also be used a marker in this fashion. It also highlights the role Ribo-Seq can have in the discovery of alternative transcripts.
Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis
Proceedings of the National Academy of Sciences, 2014; 111(1), pp.E203-E212.
Juntawong, P., Girke, T., Bazin, J. and Bailey-Serres, J.
Translational control allows for dynamic responses to varying environmental conditions (such as hypoxia, dehydration, cold, and salinity), and is essential for plant survival. Indeed, within Arabidopsis seedlings, the proportion of mRNA undergoing translation at any one point can range from <10%, to 95% under normal growth conditions. In this paper, the authors utilised ribosome profiling techniques to investigate the mechanisms of translational control under hypoxic stress conditions in Arabidopsis thaliana seedlings.
- Under hypoxic conditions, there was an obvious decrease in polysome complexes, concomitant with an increase in monosomes, indicative of decreased overall translation. There was also a general decrease in ribosome coverage at the initiation and stop codon regions.
- Hypoxia also induced significant changes in translational efficiency (TE), with 252 transcripts upregulated, and 1,645 downregulated. The translational repressed genes were enriched for proteins associated with translation (such as ribosomal proteins). Interestingly, mRNAs associated with increased transcription under hypoxic conditions did not have particularly increased ribosome recruitment/TE as compared to normoxic conditions.
- In analysing a number of genes with the presence of upstream ORFs (uORFs), it was found that uORFs appear to have a lower ribosome occupancy under hypoxic conditions, with a corresponding increase in the ribosome occupancy of the main ORF.
- It was observed that hypoxia-induced intron retention events occurred in a number of mRNA transcripts, especially within genes encoding splicing factors and circadian clock proteins.
This analysis demonstrates that plants display great variability in the regulatory mechanisms utilised to respond to stress, at both the transcriptional and translational level. A greater understanding of these mechanisms, and the particular transcripts that they target, may be utilised to develop strains with greater resistance to such hypoxic conditions.
