Abstract
BackgroundThe non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma.ResultsHere, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5’terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated.ConclusionsCombined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
Highlights
The non-coding small RNA tRNA-derived fragment (tRF) and phasiRNAs exert important roles in plant growth, development and stress resistances
In addition to participating in protein synthesis, tRNA has a variety of non-canonical functions, such as biological processes involved in cell proliferation, differentiation, apoptosis, and stress response [42, 46]. tRF, tRNA-derived fragment, is a class of non-coding small RNA (sRNA), formed tRNA precursors or mature bodies by specific endonucleases activities under precise regulation
The research by Alves et al [4] shown that the production mechanism of tRF in Arabidopsis thaliana is different from that of miRNA, not depending on DCL proteins, but the specific mechanism is not yet clear, it is speculated that S-like Ribonuclease 1 (RNS1) may be involved in the formation of tRF; co-immunoprecipitation experiments showed that both animal and plant tRF could participate in RNAi in combination with AGO protein family, and could regulate gene expression and protein synthesis through interaction with other sRNA
Summary
The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. By binding with Argonaute (AGO) protein and targeting target RNA, it exerts a negative post-transcriptional regulation function and plays an important role in plant growth and development, stress response and epigenetic modification [20]. The research by Alves et al [4] shown that the production mechanism of tRF in Arabidopsis thaliana is different from that of miRNA, not depending on DCL proteins, but the specific mechanism is not yet clear, it is speculated that S-like Ribonuclease 1 (RNS1) may be involved in the formation of tRF; co-immunoprecipitation experiments showed that both animal and plant tRF could participate in RNAi in combination with AGO protein family, and could regulate gene expression and protein synthesis through interaction with other sRNA. The method to predict target genes of tRF is still not accurate
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