TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.

Identifying transcription factor (TFs) cooperation controlling target gene expression is still an arduous challenge. The accuracy of current methods at genome scale significantly drops with the increase in number of genes, which limits their applicability to more complex genomes, like animals and plants. Here, we developed an algorithm, TransDetect, able to predict TF combinations controlling the expression level of a given gene. TransDetect was used to identify novel TF modules regulating the expression of Arabidopsis (Arabidopsis thaliana) phosphate transporter PHO1;H3 comprising MYB15, MYB84, bHLH35, and ICE1. These TFs were confirmed to interact between themselves and with the PHO1;H3 promoter. Phenotypic and genetic analyses of TF mutants enable the organization of these four TFs and PHO1;H3 in a new gene regulatory network controlling phosphate accumulation in zinc-dependent manner. This demonstrates the potential of TransDetect to extract directionality in nondynamic transcriptomes and to provide a blueprint to identify gene regulatory network involved in a given biological process.

LPCAT1 controls phosphate homeostasis in a zinc-dependent manner.

All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation.

The Involvement of OsPHO1;1 in the Regulation of Iron Transport Through Integration of Phosphate and Zinc Deficiency Signaling.

Plants survival depends on their ability to cope with multiple nutrient stresses that often occur simultaneously, such as the limited availability of essential elements inorganic phosphate (Pi), zinc (Zn), and iron (Fe). Previous research has provided information on the genes involved in efforts by plants to maintain homeostasis when a single nutrient (Pi, Zn, or Fe) is depleted. Recent findings on nutritional stress suggest that plant growth capacity is influenced by a complex tripartite interaction between Pi, Zn, and Fe homeostasis. However, despite its importance, how plants integrate multiple nutritional stimuli into complex developmental programs, and which genes are involved in this tripartite (Pi ZnFe) interaction is still not clear. The aim of this study was to examine the physiological and molecular responses of rice (Oriza sativa L.) to a combination of Pi, Zn, and/or Fe deficiency stress conditions. Results showed that Fe deficiency had the most drastic single-nutrient effect on biomass, while the Zn deficiency-effect depended on the presence of Pi in the medium. Interestingly, the observed negative effect of Fe starvation was alleviated by concomitant Pi or PiZn depletion. Members of the OsPHO1 family showed a differential transcriptional regulation in response PiZnFe combinatory stress conditions. Particularly, the transcripts of the OsPHO1;1 sense and its natural antisense cis-NatPHO1;1 showed the highest accumulation under PiZn deficiency. In this condition, the Ospho1;1 mutants showed over-accumulation of Fe in roots compared to wild type plants. These data reveal coordination between pathways involved in Fe transport and PiZn signaling in rice which involves the OsPHO1; 1, and support the hypothesis of a genetic basis for Pi, Zn, and Fe signaling interactions in plants.

Phosphate/zinc interaction analysis in two lettuce varieties reveals contrasting effects on biomass, photosynthesis, and dynamics of Pi transport.

Inorganic phosphate (Pi) and Zinc (Zn) are essential nutrients for normal plant growth. Interaction between these elements has been observed in many crop plants. Despite its agronomic importance, the biological significance and genetic basis of this interaction remain largely unknown. Here we examined the Pi/Zn interaction in two lettuce (Lactuca sativa) varieties, namely, "Paris Island Cos" and "Kordaat." The effects of variation in Pi and Zn supply were assessed on biomass and photosynthesis for each variety. Paris Island Cos displayed better growth and photosynthesis compared to Kordaat under all the conditions tested. Correlation analysis was performed to determine the interconnectivity between Pi and Zn intracellular contents in both varieties. Paris Island Cos showed a strong negative correlation between the accumulation levels of Pi and Zn in shoots and roots. However, no relation was observed for Kordaat. The increase of Zn concentration in the medium causes a decrease in dynamics of Pi transport in Paris Island Cos, but not in Kordaat plants. Taken together, results revealed a contrasting behavior between the two lettuce varieties in terms of the coregulation of Pi and Zn homeostasis and provided evidence in favor of a genetic basis for the interconnection of these two elements.