Root Cell-Specific Regulators of Phosphate-Dependent Growth

Abstract

Cellular specialization in abiotic stress responses is an important regulatory feature driving plant acclimation. Our in silico approach of iterative coexpression, interaction, and enrichment analyses predicted root cell-specific regulators of phosphate starvation response networks in Arabidopsis (Arabidopsis thaliana). This included three uncharacterized genes termed Phosphate starvation-induced gene interacting Root Cell Enriched (PRCE1, PRCE2, and PRCE3). Root cell-specific enrichment of 12 candidates was confirmed in promoter-GFP lines. T-DNA insertion lines of 11 genes showed changes in phosphate status and growth responses to phosphate availability compared with the wild type. Some mutants (cbl1, cipk2, prce3, and wdd1) displayed strong biomass gain irrespective of phosphate supply, while others (cipk14, mfs1, prce1, prce2, and s6k2) were able to sustain growth under low phosphate supply better than the wild type. Notably, root or shoot phosphate accumulation did not strictly correlate with organ growth. Mutant response patterns markedly differed from those of master regulators of phosphate homeostasis, PHOSPHATE STARVATION RESPONSE1 (PHR1) and PHOSPHATE2 (PHO2), demonstrating that negative growth responses in the latter can be overcome when cell-specific regulators are targeted. RNA sequencing analysis highlighted the transcriptomic plasticity in these mutants and revealed PHR1-dependent and -independent regulatory circuits with gene coexpression profiles that were highly correlated to the quantified physiological traits. The results demonstrate how in silico prediction of cell-specific, stress-responsive genes uncovers key regulators and how their manipulation can have positive impacts on plant growth under abiotic stress.Forward and reverse genetics are powerful approaches for the discovery and characterization of gene function. While forward genetics is greatly facilitated by next-generation sequencing-assisted mapping, it is still limited by the design of appropriate screens that involve tens of thousands of plants. Conversely, reverse genetics involves phenotypic characterization of defined mutants, hence attributing the phenotype to the mutation (Winkler et al., 1998;Krysan et al., 1999). The preeminent model plant, Arabidopsis (Arabidopsis thaliana), has an extensive mutant library with substantial genome coverage (Sessions et al., 2002;Rosso et al., 2003), making reverse genetics an attractive strategy for investigating gene function (WilsonSánchez et al., 2014). A challenge of reverse genetics is selecting candidates that are biologically relevant to the field of research. One approach is to identify these from large-scale data sets, which are increasingly being generated in the postgenomics era (Ajjawi et al., 2010). Molecular profiling of genotypes on the omics scale has been carried out extensively. However, these studies tend to sample whole plants or plant organs, masking more subtle responses that occur within discrete cell populations. Fluorescence-activated cell sorting (FACS;Birnbaum et ...

Genes involved in stress signals: the CBLs-CIPKs network in cold tolerant Solanum commersonii

“…By contrast, other CIPK genes were abundantly expressed in certain tissues. For example, ScCIPK4 was mainly expressed in roots, as also reported Linn et al (2017) in Arabidopsis whereas the expression of ScCIPK25 was detected in flowers and roots, consistent with data by Meena et al (2018).…”

SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis

“…Compared with the wild type, all mutant lines tested displayed lower shoot biomass under optimal growth conditions ( Fig. 4B, P-replete), asserting that the maintenance of P i homeostasis is linked to plant fitness (Rouached et al, 2011;Linn et al, 2017). Mutants were not impaired in root growth (Fig.…”

“…4; Supplemental Fig. S7D; Aung et al, 2006;Bari et al, 2006;Linn et al, 2017). Common effects on PSR gene expression are still unexpected, given that PHO2 function in roots has been primarily associated with controlling trafficking of PHT1;1/4 transporters and PHO1 exporter from the endoplasmic reticulum to the plasma membrane via its ubiquitin E2 conjugase activity Figure 11.…”

“…Total RNA isolation and cDNA synthesis for quantitative PCR were performed as described in Linn et al (2017). Quantitative PCR and threshold cycle (Ct) determination were performed using a fluorescence baseline setting of 0.3 (QuantStudio 12K Flex Real-Time PCR System, Applied Biosystems).…”

Phosphate Starvation Alters Abiotic-Stress-Induced Cytosolic Free Calcium Increases in Roots

“…The Pi deficiency response is orchestrated by intricate signaling networks, involving hormones, nutrient cross talk, and transcriptional and translational feedback loops (for review, see Abel, 2017;Chien et al, 2018). Ca 2+ has been hypothesized to be involved as a signal transducer (Chiou and Lin, 2011;Linn et al, 2017;Chien et al, 2018), but this has not been confirmed to date.…”