Exposure to High-Intensity Light Systemically Induces Micro-Transcriptomic Changes in Arabidopsis thaliana Roots

Abstract

In full sunlight, plants often experience a light intensity exceeding their photosynthetic capacity and causing the activation of a set of photoprotective mechanisms. Numerous reports have explained, on the molecular level, how plants cope with light stress locally in photosynthesizing leaves; however, the response of below-ground organs to above-ground perceived light stress is still largely unknown. Since small RNAs are potent integrators of multiple processes including stress responses, here, we focus on changes in the expression of root miRNAs upon high-intensity-light (HL) stress. To achieve this, we used Arabidopsis thaliana plants growing in hydroponic conditions. The expression of several genes that are known as markers of redox changes was examined over time, with the results showing that typical HL stress signals spread to the below-ground organs. Additionally, micro-transcriptomic analysis of systemically stressed roots revealed a relatively limited reaction, with only 17 up-regulated and five down-regulated miRNAs. The differential expression of candidates was confirmed by RT-qPCR. Interestingly, the detected differences in miRNA abundance disappeared when the roots were separated from the shoots before HL treatment. Thus, our results show that the light stress signal is induced in rosettes and travels through the plant to affect root miRNA levels. Although the mechanism of this regulation is unknown, the engagement of miRNA may create a regulatory platform orchestrating adaptive responses to various simultaneous stresses. Consequently, further research on systemically HL-regulated miRNAs and their respective targets has the potential to identify attractive sequences for engineering stress tolerance in plants.

Transcriptome Analysis Reveals Roles of Anthocyanin- and Jasmonic Acid-Biosynthetic Pathways in Rapeseed in Response to High Light Stress

“…Transcriptome analysis of leaves of rapeseed seedlings exposed to HL stress for 16 h revealed 7390 DEGs ( Figure 2 ), indicating a considerable change in gene expression under HL stress as observed in other plant species like Panax ginseng , A. thaliana and Begonia semperflorens [ 66 , 67 , 68 ]. Furthermore, GO analysis demonstrated that many GO terms related to photosynthesis were most enriched with DEGs ( Figure 3 ).…”

Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function

“…Since miRNAs are thought to influence circadian controlled processes ( 55 , 56 ) and are common in coding regions, we tested the possibility that these k -mers could represent miRNAs by aligning them (plus the surrounding sequence) to mature ath-miRNA sequences to identify matches (see Materials and Methods ). Two of the four k- mers matched miRNA sequences that were associated with developmental timing ( 57 ) and chloroplast biogenesis ( 58 ). Therefore, for a subset of transcripts, the k -mers could represent putative miRNA binding sites that have been experimentally linked to circadian, regulated processes, although this only accounts for a small proportion of the transcripts ( SI Appendix , Table S5 ).…”

Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function

“…Since miRNAs are thought to influence circadian controlled processes [46,47] and are common in coding regions, we tested the possibility that these k -mers could represent miRNAs by aligning them (plus surrounding sequence) to mature ath-miRNA sequences to identify possible matches (see Methods). Two of the four k- mers and their flanking sequence matched miRNA sequences that were associated with developmental timing [48] and chloroplast biogenesis [49]. Therefore, for a subset of transcripts, the k -mers could represent putative miRNA binding sites that have been experimentally linked to circadian regulated processes, although this only accounts for a small proportion of the transcripts (Table S5).…”