Abstract
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits. Except for the known miRNAs, 36 putative novel miRNAs, 6 trans-acting short interfering RNAs (ta-siRNAs), and 958 natural antisense small interfering RNAs (nat-siRNAs) were also found in our results, which enriched the tomato small RNAs repository. Among these small RNAs, 9 miRNAs, and 12 nat-siRNAs were differentially expressed between the wild and transgenic tomato fruits significantly. A large amount of target genes of the small RNAs were identified and some of them were involved in ethylene pathway, including AP2 TFs, auxin response factors, F-box proteins, ERF TFs, APETALA2-like protein, and MADS-box TFs. Degradome sequencing further confirmed the targets of miRNAs and six novel targets were also discovered. Furthermore, a regulatory model which reveals the regulation relationships between the small RNAs and their targets involved in ethylene signaling was set up. This work provides basic information for further investigation of the function of small RNAs in ethylene pathway and fruit ripening.
Highlights
Small RNAs are a class of non-coding endogenous RNAs ranged from 20 to 24 nucleotides that play essential roles in plant growth and development, signal transduction, response to biotic and abiotic stresses and other biological processes (Rhoades et al, 2002; Jones-Rhoades et al, 2006; Tomato Genome Consortium, 2012)
The small RNAs were categorized into miRNAs, ribosomal (r) RNAs, transfer (t) RNAs, small nuclear RNAs, small nucleolar RNAs, repeat regions, exon and intron RNA based on genomic location and function analysis (Table 1)
It could clearly been seen that miR394, miRZ131, miR172, miR8737, miR319, miR159, miR160, and nat-small-interfering RNAs (siRNAs)-G2001 to nat-siRNA-G2017 as well as their target genes such as auxin response factors, ethylene-responsive transcription factors and GAMYB were involved in ethylene signal pathway. These results indicate that the network of miRNAs are quite complicated, and elucidation of the molecular mechanisms underlying the interplay between miRNA and their target genes involved in ethylene pathway requires further study
Summary
Small RNAs are a class of non-coding endogenous RNAs ranged from 20 to 24 nucleotides (nt) that play essential roles in plant growth and development, signal transduction, response to biotic and abiotic stresses and other biological processes (Rhoades et al, 2002; Jones-Rhoades et al, 2006; Tomato Genome Consortium, 2012). Recent studies showed that small RNAs can negatively regulate gene expression at the post-transcriptional level based on two possible mechanisms: transcript cleavage and translational repression (Sunkar et al, 2007; Couzigou and Combier, 2016). Increasing studies showed that small RNAs are involved in regulating ethylene signal transduction (Pilcher et al, 2007; Moxon et al, 2008; Zhang et al, 2011; Zuo et al, 2012). It has been reported that the expression of genes that encode miRNAs is regulated at the transcriptional level by various transcriptional factors (Yant et al, 2010; Baek et al, 2013). EIN3, a key transcription factor in ethylene signaling, directly binds to the promoter region of miR164 and represses its transcription (Li et al, 2013)
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