Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing

Abstract

Recent studies have demonstrated the important role of plant microRNAs (miRNAs) under nutrient deficiencies. In this study, deep sequencing of Arabidopsis (Arabidopsis thaliana) small RNAs was conducted to reveal miRNAs and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6 to 1.2 million unique sequence tags from each Pi-sufficient or Pi-deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778, miR827, and miR2111 was induced, whereas the expression of miR169, miR395, and miR398 was repressed. We found cross talk coordinated by these miRNAs under different nutrient deficiencies. In addition to miRNAs, we identified one Pi starvation-induced DICER-LIKE1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5# end of tRNA and expressed at a high level in Pi-starved roots. Importantly, we observed an increased abundance of TAS4-derived trans-acting small interfering RNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(2) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs.

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…The presence of tRNA-derived RNA fragments (Lee et al 2009) has been detected also in plants Hackenberg et al 2012;Hsieh et al 2009) as well as their putative target genes (Guilherme Loss-…”

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

“…The existence of miRNAdependent pathway in distinct aspects of Pi homeostasis in these two species may suggest a species-specific pathway where many unannotated transcripts may play significant roles. It has been reported that miR2111 may target the E3 ligase gene and a calcineurin-like phosphoesterase gene under −P stress (Hsieh et al 2009). Additionally, miRNAs such as miR169, miR395, and miR398, which respond to various nutritional stresses, were also downregulated in response to Pi stress (Hsieh et al 2009).…”

“…It has been reported that miR2111 may target the E3 ligase gene and a calcineurin-like phosphoesterase gene under −P stress (Hsieh et al 2009). Additionally, miRNAs such as miR169, miR395, and miR398, which respond to various nutritional stresses, were also downregulated in response to Pi stress (Hsieh et al 2009). Therefore, some of the unannotated transcripts detected here including nonprotein coding transcripts and small RNAs may have important functions in the signaling of plant root responses to changing Pi concentrations and the coordination of homeostatic pathways of Pi and other nutrients.…”

Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation

“…genes, and these analyses have also contributed to our understanding of the global response to Pi deficiency (23)(24)(25).…”