Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice.

Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.

Gene regulatory circuitry of plant-environment interactions: scaling from cells to the field.

Plant growth and development is the product of layers of sensing and regulation that are modulated by multifactorial environmental cues. Innovations in genomics currently allow gene regulatory control to be quantified at multiple scales and high resolution in defined cell populations and even in individual cells or nuclei in plants. The application of these 'omic technologies in highly controlled, as well as field environments is revolutionizing the recognition of factors critical to spatial and temporal responses to single or multiple environmental cues. Within and pan-species comparisons illuminate deeply conserved circuitry and targets of selection. This knowledge can benefit the breeding and engineering of crops with greater resilience to climate variability and the ability to augment nutrition through plant-microbial interactions.

Photoprotection during iron deficiency is mediated by the bHLH transcription factors PYE and ILR3.

Iron (Fe) is an essential micronutrient whose availability is limiting in many soils. During Fe deficiency, plants alter the expression of many genes to increase Fe uptake, distribution, and utilization. In a genetic screen for suppressors of Fe sensitivity in the E3 ligase mutant bts-3, we isolated an allele of the bHLH transcription factor (TF) ILR3, ilr3-4 We identified a striking leaf bleaching phenotype in ilr3 mutants that was suppressed by limiting light intensity, indicating that ILR3 is required for phototolerance during Fe deficiency. Among its paralogs that are thought to be partially redundant, only ILR3 was required for phototolerance as well as repression of genes under Fe deficiency. A mutation in the gene-encoding PYE, a known transcriptional repressor under Fe deficiency, also caused leaf bleaching. We identified singlet oxygen as the accumulating reactive oxygen species (ROS) in ilr3-4 and pye, suggesting photosensitivity is due to a PSII defect resulting in ROS production. During Fe deficiency, ilr3-4 and pye chloroplasts retain normal ultrastructure and, unlike wild type (WT), contain stacked grana similar to Fe-sufficient plants. Additionally, we found that the D1 subunit of PSII is destabilized in WT during Fe deficiency but not in ilr3-4 and pye, suggesting that PSII repair is accelerated during Fe deficiency in an ILR3- and PYE-dependent manner. Collectively, our results indicate that ILR3 and PYE confer photoprotection during Fe deficiency to prevent the accumulation of singlet oxygen, potentially by promoting reduction of grana stacking to limit excitation and facilitate repair of the photosynthetic machinery.

BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana.

Iron (Fe) is required for plant health, but it can also be toxic when present in excess. Therefore, Fe levels must be tightly controlled. The Arabidopsis thaliana E3 ligase BRUTUS (BTS) is involved in the negative regulation of the Fe deficiency response and we show here that the two A. thaliana BTS paralogs, BTS LIKE1 (BTSL1) and BTS LIKE2 (BTSL2) encode proteins that act redundantly as negative regulators of the Fe deficiency response. Loss of both of these E3 ligases enhances tolerance to Fe deficiency. We further generated a triple mutant with loss of both BTS paralogs and a partial loss of BTS expression that exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects. Finally, we identified a mutant carrying a novel missense mutation of BTS that exhibits an Fe deficiency response in the root when grown under both Fe-deficient and Fe-sufficient conditions, leading to Fe toxicity when plants are grown under Fe-sufficient conditions.

OPT3 is a component of the iron-signaling network between leaves and roots and misregulation of OPT3 leads to an over-accumulation of cadmium in seeds.

Plants and seeds are the main dietary sources of zinc, iron, manganese, and copper, but are also the main entry point for toxic elements such as cadmium into the food chain. We report here that an Arabidopsis oligopeptide transporter mutant, opt3-2, over-accumulates cadmium (Cd) in seeds and roots but, unexpectedly, under-accumulates Cd in leaves. The cadmium distribution in opt3-2 differs from iron, zinc, and manganese, suggesting a metal-specific mechanism for metal partitioning within the plant. The opt3-2 mutant constitutively up-regulates the Fe/Zn/Cd transporter IRT1 and FRO2 in roots, indicative of an iron-deficiency response. No genetic mutants that impair the shoot-to-root signaling of iron status in leaves have been identified. Interestingly, shoot-specific expression of OPT3 rescues the Cd sensitivity and complements the aberrant expression of IRT1 in opt3-2 roots, suggesting that OPT3 is required to relay the iron status from leaves to roots. OPT3 expression was found in the vasculature with preferential expression in the phloem at the plasma membrane. Using radioisotope experiments, we found that mobilization of Fe from leaves is severely affected in opt3-2, suggesting that Fe mobilization out of leaves is required for proper trace-metal homeostasis. When expressed in yeast, OPT3 does not localize to the plasma membrane, precluding the identification of the OPT3 substrate. Our in planta results show that OPT3 is important for leaf phloem-loading of iron and plays a key role regulating Fe, Zn, and Cd distribution within the plant. Furthermore, ferric chelate reductase activity analyses provide evidence that iron is not the sole signal transferred from leaves to roots in leaf iron status signaling.

Tonoplast-localized Abc2 transporter mediates phytochelatin accumulation in vacuoles and confers cadmium tolerance.

Phytochelatins mediate tolerance to heavy metals in plants and some fungi by sequestering phytochelatin-metal complexes into vacuoles. To date, only Schizosaccharomyces pombe Hmt1 has been described as a phytochelatin transporter and attempts to identify orthologous phytochelatin transporters in plants and other organisms have failed. Furthermore, recent data indicate that the hmt1 mutant accumulates significant phytochelatin levels in vacuoles, suggesting that unidentified phytochelatin transporters exist in fungi. Here, we show that deletion of all vacuolar ABC transporters abolishes phytochelatin accumulation in S. pombe vacuoles and abrogates (35)S-PC(2) uptake into S. pombe microsomal vesicles. Systematic analysis of the entire S. pombe ABC transporter family identified Abc2 as a full-size ABC transporter (ABCC-type) that mediates phytochelatin transport into vacuoles. The S. pombe abc1 abc2 abc3 abc4 hmt1 quintuple and abc2 hmt1 double mutant show no detectable phytochelatins in vacuoles. Abc2 expression restores phytochelatin accumulation into vacuoles and suppresses the cadmium sensitivity of the abc quintuple mutant. A novel, unexpected, function of Hmt1 in GS-conjugate transport is also shown. In contrast to Hmt1, Abc2 orthologs are widely distributed among kingdoms and are proposed as the long-sought vacuolar phytochelatin transporters in plants and other organisms.