Investigation
Root development: role of flavonols, an antioxidant that regulate cell division and differentiation.
One of the challenges in our lab is to identify new genes and natural compounds that improve the growth of the root system under low nutrient availability, specifically under low phosphate (Pi) or low nitrate (N), two macronutrients whose shortage severely limits agricultural production. One of the problems/limitations in root biology study in the last years has been that plants are grown in many cases with the root system in presence of light, a condition that limits root growth and responses. To identify root variability and novel genes associated with the response to a particular environment, we are using a new cultivation system called D-Root (Fig. 1, video 1, Utility Patent), which allow us to cultivate plants with the root system in darkness while shoot grows in a normal photoperiodic illumination, simulating natural condition (Silva-Navas et al., 2015). The D-Root is a methacrylate box designed to fit an in vitro plate (12x12 cm or 24x24 cm cultivation plates). It also has a methacrylate comb or insert to block partially the light coming from the top (see Fig. 1). Using this system, we have shown that root light avoidance (root growth opposite to the light focus) is mediated by flavonols. This compounds also acts as integrating molecules in the root meristem to balance the proliferating and differentiating pathway by cross-working with the auxin/cytokinin responses and the oxygen reactive species H2O2/O2- to stablish a correct zonation in the root tip (Figure 2) (Silva-Navas et al., 2016).
Identification of Natural substances that regulates root growth
Another project in the lab is focused in understanding the role of BiAux, a novel metabolite identified specifically in roots. We have been able to chemically synthesize BiAux, and application of this compound to plants (Arabidopsis or tomato) significantly increased the size of the root system, mainly by generating more and larger lateral roots, and promoting plant growth and flowering time. BiAux treatment increases expression of the SKP2B::GUS, a lateral root marker, and DR5::GUS, an auxin response marker (Fig. 3). Preliminary results seem to indicate that BiAux acts as a modulator of the auxin receptor sensitivity, mainly of TIR1, AFB1 and AFB3 co-receptors. At present, we are exploring the molecular mode of action of BiAux by protein-ligand modelling and directed mutagenesis of co-receptors.
Root responses to Phosphate starvation
Using the D-Root device, we have found that root responses to Pi starvation are significantly different to previously described by several groups (Fig. 4). These differences prompted us to study this response in dark-grown roots. A transcriptomic analysis by RNA-seq identified a large number of genes that are deregulated in response to Pi deficiency that had not been previously identified in other similar experiments, likely by the negative influence of light. We have found that Pi starvation response in roots is controlled by the balance of different hormones (Fig. 5). In this regard, we found that different isomers of cytokinin (cis-, trans-zeatin) have specific roles, controlling differentially gene expression, cell division and root growth.
Plants modulate molecular responses to adapt development to the surrounding environment. The molecular function of cell types during adaptation to Pi starvation is unknown but might involve cellular specialization based on morphological changes. We are analyzing gene expression (transcriptome) and translation (translatome) during Pi starvation response at the cell type level, reconstruct a functional network of cellular adaptation and identify regulators required to sustain plant growth and Pi uptake. This information will be used to generate a transcription/translation map of the Pi starvation response in roots.
Finally, using the D-Root, we are carrying out a screening of Pi accumulation in different Arabidopsis ecotypes. We have identified one ecotype that seems to accumulate more than 5-fold than Columbia. We are also screening for beneficial microbes that enhance plant growth during Pi starvation, mainly focused on fungus endophytes.
Effect of climate change in plant nutrition and productivity
Recently we have initiated a novel line of research aimed to study the effect of climate change on root growth and function. We have engineered a novel device to simulate soil condition in a warming environment to analyze plants in vitro or in the greenhouse at high temperatures. Preliminary data showed that soil (nutrient, microorganism community, humidity, etc) is important for whole plant adaptation to heat stress. We are evaluating the effect of high temperatures on nutrient uptake and its correlation with productivity.
