Comparative expression profiling reveals a role of the root apoplast in local phosphate response

Abstract

BackgroundPlant adaptation to limited phosphate availability comprises a wide range of responses to conserve and remobilize internal phosphate sources and to enhance phosphate acquisition. Vigorous restructuring of root system architecture provides a developmental strategy for topsoil exploration and phosphate scavenging. Changes in external phosphate availability are locally sensed at root tips and adjust root growth by modulating cell expansion and cell division. The functionally interacting Arabidopsis genes, LOW PHOSPHATE RESPONSE 1 and 2 (LPR1/LPR2) and PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2), are key components of root phosphate sensing. We recently demonstrated that the LOW PHOSPHATE RESPONSE 1 - PHOSPHATE DEFICIENCY RESPONSE 2 (LPR1-PDR2) module mediates apoplastic deposition of ferric iron (Fe3+) in the growing root tip during phosphate limitation. Iron deposition coincides with sites of reactive oxygen species generation and triggers cell wall thickening and callose accumulation, which interfere with cell-to-cell communication and inhibit root growth.ResultsWe took advantage of the opposite phosphate-conditional root phenotype of the phosphate deficiency response 2 mutant (hypersensitive) and low phosphate response 1 and 2 double mutant (insensitive) to investigate the phosphate dependent regulation of gene and protein expression in roots using genome-wide transcriptome and proteome analysis. We observed an overrepresentation of genes and proteins that are involved in the regulation of iron homeostasis, cell wall remodeling and reactive oxygen species formation, and we highlight a number of candidate genes with a potential function in root adaptation to limited phosphate availability. Our experiments reveal that FERRIC REDUCTASE DEFECTIVE 3 mediated, apoplastic iron redistribution, but not intracellular iron uptake and iron storage, triggers phosphate-dependent root growth modulation. We further highlight expressional changes of several cell wall-modifying enzymes and provide evidence for adjustment of the pectin network at sites of iron accumulation in the root.ConclusionOur study reveals new aspects of the elaborate interplay between phosphate starvation responses and changes in iron homeostasis. The results emphasize the importance of apoplastic iron redistribution to mediate phosphate-dependent root growth adjustment and suggest an important role for citrate in phosphate-dependent apoplastic iron transport. We further demonstrate that root growth modulation correlates with an altered expression of cell wall modifying enzymes and changes in the pectin network of the phosphate-deprived root tip, supporting the hypothesis that pectins are involved in iron binding and/or phosphate mobilization.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0790-8) contains supplementary material, which is available to authorized users.

Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate

“…Transcriptomic analysis of Pideprived stop1 and almt1 seedlings showed that malate treatment reactivates the low-Pi responsiveness of genes that encode extracellular proteins involved in cell-wall modification and ROS homeostasis, such as peroxidases (34). Our transcriptomic results confirm a previously reported role of apoplastic peroxidases in the Pi-starvation response (33), and highlight the role of malate secretion in the cell-wall remodeling processes potentially involved in the changes of Arabidopsis root system architecture induced by low Pi availability. In this context, the finding that UPBEAT1, a transcription factor that modulates the transition from cell proliferation to cell differentiation in the RAM by repressing peroxidase genes (37), is repressed in response to Pideficiency conditions and the fact its expression is altered in stop1 and almt1, support the notion that ROS generation plays an important role in the root response to Pi deprivation.…”

“…Interestingly, using SUBA, a subcellular prediction tool (35), we found that 30% of proteins encoded by genes whose responsiveness to low Pi is restored by malate treatment in stop1 and almt1 Pi-deprived seedlings are targeted to the apoplast or extracellular region (Fig. 6B), confirming a previous study in which a major role of the apoplast in the root response to Pi starvation was highlighted (33). Furthermore, an additional 16% of genes are targeted to the plasma membrane (Fig.…”

“…Our data suggest the existence of a STOP1, ALMT1, and LPR1 coordinated redox mechanism that involves Fe +3 deposition in the apoplast of RAM cells of seedlings exposed to low Pi. ALMT1 is transcriptionally up-regulated in a similar fashion in WT and lpr1 mutants (33), confirming that LPR1 acts downstream of the STOP1/ALMT1 low-Pi regulatory node.…”

“…4B and 6C). A recent report on the interplay between the transcriptional activation of genes coding for extracellular enzymes and iron redistribution in the apoplast in response to Pi deprivation highlighted the role of the apoplast in the Pi-starvation response (33). Transcriptomic analysis of Pideprived stop1 and almt1 seedlings showed that malate treatment reactivates the low-Pi responsiveness of genes that encode extracellular proteins involved in cell-wall modification and ROS homeostasis, such as peroxidases (34).…”

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

“…In Pi-deficient plants, iron acquisition genes are generally down-regulated to compensate for increased iron levels (Misson et al, 2005;Lan et al, 2012). Down-regulation of iron acquisition genes is a consequence of oxidatively precipitated iron, which is deposited in the meristematic and elongation zones of the root as a prerequisite of Pi deficiency-induced determinacy of primary root growth (Müller et al, 2015;Hoehenwarter et al, 2016, Mora-Macías et al, 2017. While a molecular function has yet to be assigned to the two IRPs, bHLH39 was shown to form a heterodimer with the master regulator of iron homeostasis FIT (bHLH29), which controls the expression of a large subset of genes involved in the acquisition and homeostatic control of iron (Colangelo and Guerinot, 2004;Jakoby et al, 2004;Yuan et al, 2008).…”