Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing1[W][OA]

By Li-Ching Hsieh, Shu-I. Lin, Arthur Chun-Chieh Shih, June-Wei Chen, Wei-Yi Lin, C. Tseng, Wen-Hsiung Li, T. Chiou. Plant Physiology, 2009

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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(−) 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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/e3e6443dc4edae3cabf47891b430456b0c40028a

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Citations in the corpus

Biosynthesis and Regulation of Phenylpropanoids in Plants (2017, background): “…2013; Zhang and Wang, 2015). miR828 and miR858 are two miRNAs involved in the regulation of phenylpropanoid biosynthesis by targeting R2R3-MYBs (Hsieh et al., 2009; Lin et al., 2012; Luo et al., 2012; Xia et al., 2012; Zhu et al., 2012; Rock, 2013; Yang et al., 2013; Jia et al., 2015; Sharma…”
Signaling network in sensing phosphate availability in plants. (2011, background): “Furthermore, an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4siR81(−), a trans-acting siRNA that regulates the biosynthesis of anthocyanin during Pi deficiency, was revealed (46).”
Plant microRNAs: new players in functional genomics (2013, neutral): “…expression profiles could be differentiated under a variety of stress conditions including drought (Barrera-Figueroa et al. 2011; Wang et al. 2011b), cold (Zhang et al. 2009), phosphate deficiency (Hsieh et al. 2009), sulfate deficiency (Huang et al. 2010), and fungal infection (Xin et al. 2011).”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “We analyzed small RNA-Seq datasets generated from root (Hsieh et al., 2009; Breakfield et al., 2012), leaf (Yu et al.”
A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis (2010, background): “These include sumoylation [18], degradation by the proteosome, which probably involves the E2 ubiquitin conjugase-related enzyme (PHO2) [19–21], and control of Pi uptake efficiency via a phosphate transporter traffic facilitator (PHF1) [22], as well as several miRNA and antagonists (IPS1 and related”