Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

Secco, David; Jabnoune, Mehdi; Walker, Hayden; Shou, Huixia; Wu, Ping; Poirier, Yves; Whelan, James

doi:10.1105/tpc.113.117325

Cited by 276 publications

(297 citation statements)

References 70 publications

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“…4b) and in all of the 12 identified isoforms from LOC_Os12g02040 (Supplementary Table S4). Additionally, we applied our method to another publicly available RNA-Seq data set (GenBank accession number SRR1005311) generated from rRNA depleted RNA from rice roots under phosphate starvation stress conditions 37 and also found a large number of circRNAs with non-GT/AG splicing signals. In this analysis, a total of 943 circRNAs with full-length sequences were identified and only 42 contained the canonical GT/AG splicing signals (Fig.…”

Section: Alternative Circularization Of Circrnas In Ricementioning

confidence: 99%

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

et al. 2016

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Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.

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Section: Alternative Circularization Of Circrnas In Ricementioning

confidence: 99%

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

et al. 2016

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“…We showed that cellular responses that inhibit the development of new arbuscules occurred within hours of P treatment. Differential expression of thousands of rice genes was observed in shoots and roots within 1 h after P treatment (Secco et al, 2013), further indicating molecular and cellular responses that inhibit new arbuscule development within a few hours. Intriguingly, colonization can recover within a couple of days.…”

Section: Short-term P Inhibition Versus Long-term P Inhibitionmentioning

confidence: 99%

Phosphate Treatment Strongly Inhibits New Arbuscule Development But Not the Maintenance of Arbuscule in Mycorrhizal Rice Roots

et al. 2016

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ORCID IDs: 0000-0002-9997-490X (Y.K.); 0000-0001-8867-5085 (C.S.).Phosphorus (P) is a crucial nutrient for plant growth, but its availability to roots is limited in soil. Arbuscular mycorrhizal (AM) symbiosis is a promising strategy for improving plant P acquisition. However, P fertilizer reduces fungal colonization (P inhibition) and compromises mycorrhizal P uptake, warranting studies on the mechanistic basis of P inhibition. In this study, early morphological changes in P inhibition were identified in rice (Oryza sativa) using fungal cell wall staining and live-cell imaging of plant membranes that were associated with arbuscule life cycles. Arbuscule density decreased, and aberrant hyphal branching was observed in roots at 5 h after P treatment. Although new arbuscule development was severely inhibited, preformed arbuscules remained intact and longevity remained constant. P inhibition was accelerated in the rice pt11-1 mutant, which lacks P uptake from arbuscule branches, suggesting that mature arbuscules are stabilized by the symbiotic P transporter under high P condition. Moreover, P treatment led to increases in the number of vesicles, in which lipid droplets accumulated and then decreased within a few days. The development of new arbuscules resumed within by 2 d. Our data established that P strongly and temporarily inhibits new arbuscule development, but not intraradical accommodation of AM fungi.

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“…This gene induction was not only dependent on illumination, but also observed under additional stresses such as salt and drought stress. MGD genes are induced in rice also under long-term phosphate deficiency (Secco et al, 2013), making this flooding-tolerant plant an ideal model for future studies.…”

Section: Galactolipids Seem To Play No Major Role In the Survival Undmentioning

confidence: 99%

A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1

et al. 2014

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Plant responses to biotic and abiotic stresses are often very specific, but signal transduction pathways can partially or completely overlap. Here, we demonstrate that in Arabidopsis (Arabidopsis thaliana), the transcriptional responses to phosphate starvation and oxygen deficiency stress comprise a set of commonly induced genes. While the phosphate deficiency response is systemic, under oxygen deficiency, most of the commonly induced genes are found only in illuminated shoots. This jointly induced response to the two stresses is under control of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), but not of the oxygen-sensing N-end rule pathway, and includes genes encoding proteins for the synthesis of galactolipids, which replace phospholipids in plant membranes under phosphate starvation. Despite the induction of galactolipid synthesis genes, total galactolipid content and plant survival are not severely affected by the up-regulation of galactolipid gene expression in illuminated leaves during hypoxia. However, changes in galactolipid molecular species composition point to an adaptation of lipid fluxes through the endoplasmic reticulum and chloroplast pathways during hypoxia. PHR1-mediated signaling of phosphate deprivation was also light dependent. Because a photoreceptor-mediated PHR1 activation was not detectable under hypoxia, our data suggest that a chloroplast-derived retrograde signal, potentially arising from metabolic changes, regulates PHR1 activity under both oxygen and phosphate deficiency.

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Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

Cited by 276 publications

References 70 publications

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Phosphate Treatment Strongly Inhibits New Arbuscule Development But Not the Maintenance of Arbuscule in Mycorrhizal Rice Roots

A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1

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