Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays

Abstract

MicroRNAs (miRNAs) are short RNA chains (20-24 bp) which are emerging as important regulators of gene expression. miRNAs are encoded by specific genes, and in Arabidopsis, 190 genes have presently been identified. It has been shown that miR399 is essential for the phosphate starvation response, and recent studies have shown transcriptional changes in a number of additional miRNAs in response to a shortage of phosphate. In this study, global profiles of the miRNA in shoots of Arabidopsis plants grown on limited phosphate or full nutrient in combination with sucrose feed were analysed using the miRCURY LNA microRNA Array system. Furthermore, changes in miRNA transcript were compared between a mutant lacking the transcription factor phosphate starvation responses 1 (PHR1) and wild-type plants. The global analysis identified miRNAs belonging to nine families to respond to P deprivation, sucrose or PHR1. Among these, miR399d, miR827, miR866, miR391 and miR163 were most prominently induced upon P starvation, whereas miR169b/c was strongly induced in previously starved plants when provided with sufficient P and more so when combined with an addition of sucrose. This study shows that array analysis is in general agreement with data obtained by other high-throughput technologies. The array data were confirmed by real-time reverse transcriptase-polymerase chain reaction analyses of selected pri-miRNAs. Our data corroborate the implication that several miRNAs are involved in the P-starvation response and further identify miR866 and miR163 as new candidates of miRNAs associated with the regulation of the P-starvation response.

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage

“…We confirmed that the well-studied miR399 and miR827 were both upregulated by phosphate starvation, as reported previously in Arabidopsis (Fujii et al, 2005;Aung et al, 2006;Chiou et al, 2006;Hsieh et al, 2009;Pant et al, 2009;Lundmark et al, 2010) and in rice (Bari et al, 2006;Lin et al, 2010). Intriguingly, miR827 was also strongly induced by the combined stress of salt stress under conditions of potassium starvation ( Figure 6G).…”

“…Perhaps the most well-studied miRNAs that are regulated by and function during environmental stress are miR399 and miR827, both of which are induced by phosphate starvation (Fujii et al, 2005;Aung et al, 2006;Bari et al, 2006;Chiou et al, 2006;Duan et al, 2008;Pant et al, 2009;Lin et al, 2010;Lundmark et al, 2010;Kant et al, 2011). Our study confirmed this regulation ( Figure 6E) as well as the sulfur starvation induction of miR395 (Jones- ) that, to our knowledge, prior to this work had not been reported in rice.…”

“…They reported specific miRNAs showing altered expression patterns under environmental stresses such as cold, drought, salt, UV-B radiation, oxidative stress, or mechanical stress (Sunkar and Zhu, 2004;Sunkar et al, 2007;Zhou et al, 2007;Lu et al, 2008b;Zhou et al, 2008;Li et al, 2011). In addition, it has also been documented that several miRNAs are associated with nutrient homeostasis under phosphate or sulfate depletion conditions (Jones- Fujii et al, 2005;Aung et al, 2006;Bari et al, 2006;Hsieh et al, 2009;Lundmark et al, 2010;Nilsson et al, 2010). Although most of these observations were made in Arabidopsis, a few studies also reported stress-related miRNAs in rice (Oryza sativa; Bari et al, 2006;Zhao et al, 2007Zhao et al, , 2009aSanan-Mishra et al, 2009;Jian et al, 2010;Li et al, 2011).…”

Sugar Signaling in Root Responses to Low Phosphorus Availability

“…Members of the IPSI1/Mt4/At4 family of noncoding transcripts, whose expression is rapidly and specifically induced in response to P starvation, appear to bind and sequester miR399s, thereby attenuating miR399-mediated transcriptional responses to P starvation (Franco-Zorrilla et al, 2007). In addition to miR399, several other microRNA species have been implicated in regulating plant responses to low P availability (Hsieh et al, 2009;Pant et al, 2009;Gu et al, 2010;Lin et al, 2010;Lundmark et al, 2010;Zhu et al, 2010). These include miR156, miR158, miR163, miR319, miR391, miR447, miR778, miR827, miR866, and miR2111, which increase in abundance in plants during P starvation.…”

A Wheat CCAAT Box-Binding Transcription Factor Increases the Grain Yield of Wheat with Less Fertilizer Input

“…The microRNA169 (miR169) family is known to be regulated by both N and P starvation (Pant et al, 2009;Lundmark et al, 2010;Xu et al, 2011Xu et al, , 2013Zhao et al, 2011;Liang et al, 2012). Different members of this microRNA family show distinct response patterns to N or P starvation (Pant et al, 2009;Liang et al, 2012;Xu et al, 2013).…”