Reprogramming of translation in response to abiotic stress from model plant to crop
Final Report Abstract
Exposure of plants to high temperatures can have negative effects on plant growth and development. Due to global warming and the more frequent exposure of crops to temperature extremes like heat waves, the description of how plants respond to high temperatures are one of the top priorities for plant biologists. Essential for thermotolerance is the activation of heat stress (HS) response which includes the induction of expression of genes coding for proteins with thermoprotective functions such as heat shock proteins (HSPs). In addition, hundreds of other genes are transcribed. These genes code for proteins that are involved in various biological processes including hormone and secondary metabolism, and they can vary among different organs, tissues and even cell types. In addition, the synthesized pre-mRNA needs to be properly processed in order for mature mRNAs that are destined for translation to be synthesized. It has been assumed that variations in the thermotolerance among different organs at least in part are due to differences in the transcriptome regulation both at the level of transcription and pre-mRNA splicing. Here, we used tomato (Solanum lycopersicum) to examine the global changes in the transcriptome landscape that occur in different organs exposed to different temperatures and for different time points. Tomato is an important crop is an important crop worldwide and in biology a model plant for fleshy fruit development but also extensively used in heat stress related studies. We aimed to create a detailed transcriptome landscape map of the qualitative and quantitative changes on mRNAs on different tomato organs exposed to mild and strong temperature elevations. This information is important in order to identify the transcriptome dynamics in relation to the stress intensity in an organ-dependent manner. Such information is currently lacking in tomato. We employed long (Iso-Seq) and short read next generation sequencing (NGS) technologies for RNA on vegetative (leaves, roots) and reproductive (flower buds, immature and mature fruits) exposed to 25°C (control temperature), 35, 40, and 45°C for 1 hour. We were able to: (1) identify common and distinct transcriptome responses in different organs, in terms of splice variant occurrence and abundance; (2) determine changes in the dynamics that different temperatures impose in transcriptome landscape of tomato organs; (3) identify novel splice variants that can be putatively translated to protein isoforms with altered functions. The latter is important for the tomato field in general, as our results on splice variants give important insights into the tomato genome diversity. By these approaches we are able to show that: (1) there are fundamental differences in the transcriptome profile of different organs in response to heat stress, particularly on the splicing variants occurrence; (2) specific putative protein isoforms are produced under heat stress conditions that have potentially different properties and functions and by this can shape different cellular processes related to stress response and thermotolerance; (3) specific sequence motifs are associated with alternatively spliced introns, suggesting that regulation of pre-mRNA splicing is mediated by specific RNA-binding proteins that recognize these sequence motifs and therefore there are common principles for heat stress sensitive alternative splicing. Thereby, our results shed light into an important process of regulation of gene expression and provide insights into putative important thermotolerance-relevant molecular adaptation mechanisms in an important crop.
Publications
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Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures. Frontiers in Plant Science, 12.
Rosenkranz, Remus R. E.; Bachiri, Samia; Vraggalas, Stavros; Keller, Mario; Simm, Stefan; Schleiff, Enrico & Fragkostefanakis, Sotirios
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“Splicing as central regulatory element of the plant heat stress response” 4th International Caparica Conference in SPLICING 2021, 7/2021. Caparica, Portugal
Enrico Schleiff
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Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. Frontiers in Plant Science, 13.
Rosenkranz, Remus R. E.; Ullrich, Sarah; Löchli, Karin; Simm, Stefan & Fragkostefanakis, Sotirios
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“Regulation of plant acclimation to heat stress by transcription factors & splicing regulators”. EMBO: Molecular responses of plants facing climate change. 13- 17/6/2022, Montpellier, France.
Sotirios Fragkostefanakis
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“Transcription Factors and Splicing Regulators: Brothers in Arms to Survive Heat”. International Conference of Plant EcoPhysiological Adaptation Mechanisms. 09/2022 Tirana, Albania.
Sotirios Fragkostefanakis
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Crosstalk between endoplasmic reticulum and cytosolic unfolded protein response in tomato. Cell Stress and Chaperones, 28(5), 511-528.
Löchli, Karin; Torbica, Emma; Haile-Weldeslasie, Misgana; Baku, Deborah; Aziz, Aatika; Bublak, Daniela & Fragkostefanakis, Sotirios
