Heart of endosymbioses : transcriptomics reveals a conserved genetic program among arbuscular mycorrhizal, actinorhizal and legume-rhizobial symbioses

To improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. A few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. Fossil and molecular data suggest that the molecular mechanisms involved in these root nodule symbioses (RNS) have been partially recycled from more ancient and widespread arbuscular mycorrhizal (AM) symbiosis. We used a comparative transcriptomics approach to identify genes involved in establishing these 3 endosymbioses and their functioning. We analysed global changes in gene expression in AM in the actinorhizal tree C. glauca. A comparison with genes induced in AM in Medicago truncatula and Oryza sativa revealed a common set of genes induced in AM. A comparison with genes induced in nitrogen-fixing nodules of C. glauca and M. truncatula also made it possible to define a common set of genes induced in these three endosymbioses. The existence of this core set of genes is in accordance with the proposed recycling of ancient AM genes for new functions related to nodulation in legumes and actinorhizal plants

Root Responses to Heterogeneous Nitrate Availability are Mediated by trans-Zeatin in Arabidopsis Shoots

preprint déposé dans bioRxivPlants are subjected to variable nitrogen (N) availability including frequent spatial nitrate (NO3-) heterogeneity in soil. Thus, plants constantly adapt their genome expression and root physiology in order to optimize N acquisition from this heterogeneous source. These adaptations rely on a complex and long distance root-shoot-root signaling network that is still largely unknown. Here, we used a combination of reverse genetics, transcriptomic analysis, NO3- uptake experiments and hormone profiling under conditions of homogeneous or heterogeneous NO3- availability to characterize the systemic signaling involved. We demonstrate the important role of the trans-zeatin form of cytokinin (CK) in shoots, in particular using a mutant altered for ABCG14-mediated trans-zeatin-translocation from the root to theshoot, in mediating: (i) rapid long distance N-demand signaling and (ii) long term functional adaptations to heterogeneous NO3- supply, including changes in NO3- transport capacity and root growthmodifications. We also provide insights into the potential CK-dependent and independent shoot-to-root signals involved in root adaptation to heterogeneous N availability

High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings

Abstract Background High-throughput phenotyping is crucial for the genetic and molecular understanding of adaptive root system development. In recent years, imaging automata have been developed to acquire the root system architecture of many genotypes grown in Petri dishes to explore the Genetic x Environment (GxE) interaction. There is now an increasing interest in understanding the dynamics of the adaptive responses, such as the organ apparition or the growth rate. However, due to the increasing complexity of root architectures in development, the accurate description of the topology, geometry, and dynamics of a growing root system remains a challenge. Results We designed a high-throughput phenotyping method, combining an imaging device and an automatic analysis pipeline based on registration and topological tracking, capable of accurately describing the topology and geometry of observed root systems in 2D+t. The method was tested on a challenging Arabidopsis seedling dataset, including numerous root occlusions and crossovers. Static phenes are estimated with high accuracy ( R 2 = 0.996 and 0, 923 for primary and second-order roots length, respectively). These performances are similar to state-of-the-art results obtained on root systems of equal or lower complexity. In addition, our pipeline estimates dynamic phenes accurately between two successive observations ( R 2 = 0. 938 for lateral root growth). Conclusions We designed a novel method of root tracking that accurately and automatically measures both static and dynamic RSA parameters from a novel high-throughput root phenotyping platform. It has been used to characterize developing patterns of root systems grown under various environmental conditions. It provides a solid basis to explore the GxE interaction controlling the dynamics of root system architecture adaptive responses. In future work, our approach will be adapted to a wider range of imaging configurations and species

High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings

International audienceBackground: High-throughput phenotyping is crucial for the genetic and molecular understanding of adaptive root system development. In recent years, imaging automata have been developed to acquire the root system architecture of many genotypes grown in Petri dishes to explore the Genetic x Environment (GxE) interaction. There is now an increasing interest in understanding the dynamics of the adaptive responses, such as the organ apparition or the growth rate. However, due to the increasing complexity of root architectures in development, the accurate description of the topology, geometry, and dynamics of a growing root system remains a challenge. Results: We designed a high-throughput phenotyping method, combining an imaging device and an automatic analysis pipeline based on registration and topological tracking, capable of accurately describing the topology and geometry of observed root systems in 2D + t. The method was tested on a challenging Arabidopsis seedling dataset, including numerous root occlusions and crossovers. Static phenes are estimated with high accuracy (R 2 = 0.996 and 0.923 for primary and second-order roots length, respectively). These performances are similar to state-of-the-art results obtained on root systems of equal or lower complexity. In addition, our pipeline estimates dynamic phenes accurately between two successive observations (R 2 = 0.938 for lateral root growth). Conclusions: We designed a novel method of root tracking that accurately and automatically measures both static and dynamic parameters of the root system architecture from a novel high-throughput root phenotyping platform. It has been used to characterise developing patterns of root systems grown under various environmental conditions. It provides a solid basis to explore the GxE interaction controlling the dynamics of root system architecture adaptive responses. In future work, our approach will be adapted to a wider range of imaging configurations and species

Interaction between systemic nitrogen signaling and hormones, in arabidopsis

Rapid adjustment of plant physiology and development to external fluctuations is critical for sessile organism, giving a singular interest to network signaling controlling these mechanisms. Among many adaptation processes, root plasticity is primordial to optimize nutrient acquisition but relies on a complex network integrating local and systemic (root <‐> shoot) signaling. Indeed, locally, plants invest resource in soil area where nutrients are available and systemically they adjust nutrient acquisition to the whole plant demand. Our main goal is to decipher systemic signaling underlying the perception of nitrate heterogeneous provision, in Arabidopsis. Using the split‐root system, in which physically isolated root systems of the same plant were challenged with different environments, we previously demonstrated that cytokinin biosynthesis constitutes one critical component of root‐shoot‐root communication. By combining the use of cytokinin mutants with hormone measurements, transcriptomic analysis, nitrate uptake assays, and root growth measurements, we show that root to shoot trans ‐zeatin ( t Z) translocation is likely crucial for long distance signaling controlling rapid sentinel gene regulation and long‐term functional acclimation to heterogeneous nitrate supply. Interestingly, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of t Z root‐to‐shoot translocation, prompting an interesting hypothesis regarding shoot‐to‐root communication. Finally, this study also highlights t Z‐independent pathways triggered by variation into nitrogen supply

Responses to Systemic Nitrogen Signaling in Arabidopsis Roots Involve trans-Zeatin in Shoots

Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To overcome these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana. By comparing wild-type plants and mutants affected in CK biosynthesis and ABCG14-dependent root-to-shoot translocation of CK, we revealed an important role for active trans-Zeatin (tZ) in systemic N signaling. Both rapid sentinel gene regulation and long-term functional acclimation to heterogeneous NO3- supply, including NO3- transport and root growth regulation, are likely mediated by the integration of tZ content in shoots. Furthermore, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study highlights tZ-independent pathways regulating gene expression in shoots as well as NO3- uptake activity in response to total N-deprivation

Interaction between nitrate-related long-distance signaling and hormones, in Arabidopsis

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Regulatory Network behind Systemic Nitrogen Signaling, in Arabidopsis

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