Project acronym FEAR-SAP
Project Function and Evolution of Attack and Response Strategies during Allelopathy in Plants
Researcher (PI) Claude BECKER
Host Institution (HI) GREGOR MENDEL INSTITUT FUR MOLEKULARE PFLANZENBIOLOGIE GMBH
Call Details Starting Grant (StG), LS9, ERC-2016-STG
Summary In natural and agricultural habitats, plants grow in organismal communities and therefore have to compete for limited resources. Competition between different crop plants and between crops and weeds leads to losses of potential agricultural product and requires heavy use of fertilizer and herbicides, with negative effects for the environment and human health. Plants have evolved various strategies to outcompete their neighbours and to secure their access to resources; one of them is the release of toxic chemical compounds into the soil that interfere with the growth of neighbouring plants. Many of today’s major crops, such as wheat, rye and maize, produce phytotoxins. Conversely, crop species also suffer from chemical attack by other plants growing in their vicinity. Although many of the chemical compounds applied in this biochemical warfare have been identified, we know little about how they act in the target plant; neither do we understand how some plant species are able to tolerate this chemical attack.
FEAR-SAP studies the genetic architecture that underlies biochemical plant-plant interference and the evolution of weed resistance to crop-released phytotoxins. To this end it employs a comprehensive array of molecular genetics, genomics and metagenomics analyses, unprecedented in the research on plant-plant competition. The aims of FEAR-SAP are to uncover the molecular targets of plant-derived phytotoxins and to identify the genetic components that are essential for tolerance to these substances. Moreover, FEAR-SAP investigates how the microbial community that is associated with the plant might enhance efficiency of the donor and/or mediate tolerance of the target plant. Ultimately, we will use this information to explore intelligent engineering of more refined and competitive crops, which will be at the foundation of efficient and ecologically responsible weed control and improved crop rotation strategies.
Summary
In natural and agricultural habitats, plants grow in organismal communities and therefore have to compete for limited resources. Competition between different crop plants and between crops and weeds leads to losses of potential agricultural product and requires heavy use of fertilizer and herbicides, with negative effects for the environment and human health. Plants have evolved various strategies to outcompete their neighbours and to secure their access to resources; one of them is the release of toxic chemical compounds into the soil that interfere with the growth of neighbouring plants. Many of today’s major crops, such as wheat, rye and maize, produce phytotoxins. Conversely, crop species also suffer from chemical attack by other plants growing in their vicinity. Although many of the chemical compounds applied in this biochemical warfare have been identified, we know little about how they act in the target plant; neither do we understand how some plant species are able to tolerate this chemical attack.
FEAR-SAP studies the genetic architecture that underlies biochemical plant-plant interference and the evolution of weed resistance to crop-released phytotoxins. To this end it employs a comprehensive array of molecular genetics, genomics and metagenomics analyses, unprecedented in the research on plant-plant competition. The aims of FEAR-SAP are to uncover the molecular targets of plant-derived phytotoxins and to identify the genetic components that are essential for tolerance to these substances. Moreover, FEAR-SAP investigates how the microbial community that is associated with the plant might enhance efficiency of the donor and/or mediate tolerance of the target plant. Ultimately, we will use this information to explore intelligent engineering of more refined and competitive crops, which will be at the foundation of efficient and ecologically responsible weed control and improved crop rotation strategies.
Max ERC Funding
1 500 000 €
Duration
Start date: 2018-01-01, End date: 2022-12-31
Project acronym FunDiT
Project Functional Diversity of T cells
Researcher (PI) Ondrej STEPANEK
Host Institution (HI) USTAV MOLEKULARNI GENETIKY AKADEMIE VED CESKE REPUBLIKY VEREJNA VYZKUMNA INSTITUCE
Call Details Starting Grant (StG), LS6, ERC-2018-STG
Summary T cells have a central role in most adaptive immune responses, including immunity to infection, cancer, and autoimmunity. Increasing evidence shows that even resting steady-state T cells form many different subsets with unique functions. Variable level of self-reactivity and previous antigenic exposure are most likely two major determinants of the T-cell diversity. However, the number, identity, and biological function of steady-state T-cell subsets are still very incompletely understood. Receptors to ligands from TNF and B7 families exhibit variable expression among T-cell subsets and are important regulators of T-cell fate decisions. We hypothesize that pathways triggered by these receptors substantially contribute to the functional diversity of T cells.The FunDiT project uses a set of novel tools to systematically identify steady-state CD8+ T cell subsets and characterize their biological roles. The project has three complementary objectives.
(1) Identification of CD8+ T cell subsets. We will identify subsets based on single cell gene expression profiling. We will determine the role of self and foreign antigens in the formation of these subsets and match corresponding subsets between mice and humans.
(2) Role of particular subsets in the immune response. We will compare antigenic responses of particular subsets using our novel model allowing inducible expression of a defined TCR. The activity of T-cell subsets in three disease models (infection, cancer, autoimmunity) will be characterized.
(3) Characterization of key costimulatory/inhibitory pathways. We will use our novel mass spectrometry-based approach to identify receptors and signaling molecules involved in the signaling by ligands from TNF and B7 families in T cells.
The results will provide understanding of the adaptive immunity in particular disease context and resolve long-standing questions concerning the roles of T-cell diversity in protective immunity and tolerance to healthy tissues and tumors.
Summary
T cells have a central role in most adaptive immune responses, including immunity to infection, cancer, and autoimmunity. Increasing evidence shows that even resting steady-state T cells form many different subsets with unique functions. Variable level of self-reactivity and previous antigenic exposure are most likely two major determinants of the T-cell diversity. However, the number, identity, and biological function of steady-state T-cell subsets are still very incompletely understood. Receptors to ligands from TNF and B7 families exhibit variable expression among T-cell subsets and are important regulators of T-cell fate decisions. We hypothesize that pathways triggered by these receptors substantially contribute to the functional diversity of T cells.The FunDiT project uses a set of novel tools to systematically identify steady-state CD8+ T cell subsets and characterize their biological roles. The project has three complementary objectives.
(1) Identification of CD8+ T cell subsets. We will identify subsets based on single cell gene expression profiling. We will determine the role of self and foreign antigens in the formation of these subsets and match corresponding subsets between mice and humans.
(2) Role of particular subsets in the immune response. We will compare antigenic responses of particular subsets using our novel model allowing inducible expression of a defined TCR. The activity of T-cell subsets in three disease models (infection, cancer, autoimmunity) will be characterized.
(3) Characterization of key costimulatory/inhibitory pathways. We will use our novel mass spectrometry-based approach to identify receptors and signaling molecules involved in the signaling by ligands from TNF and B7 families in T cells.
The results will provide understanding of the adaptive immunity in particular disease context and resolve long-standing questions concerning the roles of T-cell diversity in protective immunity and tolerance to healthy tissues and tumors.
Max ERC Funding
1 725 000 €
Duration
Start date: 2019-01-01, End date: 2023-12-31
Project acronym HelixMold
Project Computational design of novel functions in helical proteins by deviating from ideal geometries
Researcher (PI) Gustav OBERDORFER
Host Institution (HI) TECHNISCHE UNIVERSITAET GRAZ
Call Details Starting Grant (StG), LS9, ERC-2018-STG
Summary We propose to computationally design novel ligand binding and catalytically active proteins by harnessing the high thermodynamic stability of de novo helical proteins. Tremendous progress has been made in protein design. However, the ability to robustly introduce function into genetically encodable de novo proteins is an unsolved problem. We will follow a highly interdisciplinary computational-experimental approach to address this challenge and aim to:
-Characterize to which extent we can harness the stability of parametrically designed helical bundles to introduce deviations from ideal geometry. Ensembles of idealized de novo helix bundle backbones will be generated using our established parametric design code and designed with constraints accounting for an envisioned functional site. This will be followed by detailed computational, biophysical, crystallographic and site-saturation mutagenesis analysis to isolate critical design features.
-Develop a new computational design strategy, which expands on the Crick coiled-coil parametrization and allows to rationally build non-ideal helical protein backbones at specified regions in the desired structure. This will enable us to model backbones around binding/active sites. We will design sites to bind glyphosate, for which remediation is highly needed. By using non-ideal geometries and not relying on classic heptad repeating units, we will be able to access a much larger sequence to structure space than is usually available to nature, enabling us to build more specific and more stable binding/catalytically active proteins.
-Investigate new strategies to design the first cascade reactions into de novo designs.
This research will allow functionalization of de novo designed proteins with high thermostability, extraordinary resistance to harsh chemical environments and high tolerance for organic solvents and has the potential to revolutionize how proteins for biotechnological and biomedical applications are generated.
Summary
We propose to computationally design novel ligand binding and catalytically active proteins by harnessing the high thermodynamic stability of de novo helical proteins. Tremendous progress has been made in protein design. However, the ability to robustly introduce function into genetically encodable de novo proteins is an unsolved problem. We will follow a highly interdisciplinary computational-experimental approach to address this challenge and aim to:
-Characterize to which extent we can harness the stability of parametrically designed helical bundles to introduce deviations from ideal geometry. Ensembles of idealized de novo helix bundle backbones will be generated using our established parametric design code and designed with constraints accounting for an envisioned functional site. This will be followed by detailed computational, biophysical, crystallographic and site-saturation mutagenesis analysis to isolate critical design features.
-Develop a new computational design strategy, which expands on the Crick coiled-coil parametrization and allows to rationally build non-ideal helical protein backbones at specified regions in the desired structure. This will enable us to model backbones around binding/active sites. We will design sites to bind glyphosate, for which remediation is highly needed. By using non-ideal geometries and not relying on classic heptad repeating units, we will be able to access a much larger sequence to structure space than is usually available to nature, enabling us to build more specific and more stable binding/catalytically active proteins.
-Investigate new strategies to design the first cascade reactions into de novo designs.
This research will allow functionalization of de novo designed proteins with high thermostability, extraordinary resistance to harsh chemical environments and high tolerance for organic solvents and has the potential to revolutionize how proteins for biotechnological and biomedical applications are generated.
Max ERC Funding
1 499 414 €
Duration
Start date: 2019-04-01, End date: 2024-03-31
Project acronym PhytoTrace
Project Wanted: Micronutrients! Phytosiderophore-mediated acquisition strategies in grass crops
Researcher (PI) Eva OBURGER
Host Institution (HI) UNIVERSITAET FUER BODENKULTUR WIEN
Call Details Starting Grant (StG), LS9, ERC-2018-STG
Summary Understanding how plants respond to micronutrient deficiency and which biogeochemical processes are induced at the root-soil interface, i.e. the rhizosphere, is crucial to improve crop yield and micronutrient grain content for high quality food and feed. Iron nutrition by grass species relies on the release and re-uptake of phytosiderophores, which are root exudates that form stable complexes with Fe but also other trace metals such as Zn and Cu. However, neither the importance of phytosiderophores under Zn and Cu deficient conditions nor the interplay of plant responses and rhizosphere processes are well understood as the majority of studies in the past was carried out under ‘soil-free’ hydroponic conditions. In this project, I aim to elucidate the mechanisms controlling phytosiderophore-mediated micronutrient acquisition of barley (Hordeum vulgare) under Zn, Cu, and as reference, Fe deficient conditions, with particular emphasis on soil environments. Barley is the fifth most produced crop worldwide and of great importance in regions that are characterized by harsh living conditions. In a holistic approach, my team and I will apply innovative soil-based and traditional hydroponic root exudation sampling approaches in combination with advanced plant molecular techniques to study the phytosiderophore release and uptake system under different experimental conditions. The chemical synthesis of otherwise commercially unavailable phytosiderophores in their natural and 13C-labelled form will allow us to trace their decomposition and metal solubilizing efficiency in the plant-microbe-soil system to uncover the interplay of plant genetic responses and rhizosphere processes affecting the time-window of PS-mediated MN acquisition. Moving beyond ‘soil-free’ experimental designs of the past, this project will generate key knowledge to improve selection of crops with highly efficient micronutrient acquisition traits to alleviate micronutrient malnutrition of people world-wide.
Summary
Understanding how plants respond to micronutrient deficiency and which biogeochemical processes are induced at the root-soil interface, i.e. the rhizosphere, is crucial to improve crop yield and micronutrient grain content for high quality food and feed. Iron nutrition by grass species relies on the release and re-uptake of phytosiderophores, which are root exudates that form stable complexes with Fe but also other trace metals such as Zn and Cu. However, neither the importance of phytosiderophores under Zn and Cu deficient conditions nor the interplay of plant responses and rhizosphere processes are well understood as the majority of studies in the past was carried out under ‘soil-free’ hydroponic conditions. In this project, I aim to elucidate the mechanisms controlling phytosiderophore-mediated micronutrient acquisition of barley (Hordeum vulgare) under Zn, Cu, and as reference, Fe deficient conditions, with particular emphasis on soil environments. Barley is the fifth most produced crop worldwide and of great importance in regions that are characterized by harsh living conditions. In a holistic approach, my team and I will apply innovative soil-based and traditional hydroponic root exudation sampling approaches in combination with advanced plant molecular techniques to study the phytosiderophore release and uptake system under different experimental conditions. The chemical synthesis of otherwise commercially unavailable phytosiderophores in their natural and 13C-labelled form will allow us to trace their decomposition and metal solubilizing efficiency in the plant-microbe-soil system to uncover the interplay of plant genetic responses and rhizosphere processes affecting the time-window of PS-mediated MN acquisition. Moving beyond ‘soil-free’ experimental designs of the past, this project will generate key knowledge to improve selection of crops with highly efficient micronutrient acquisition traits to alleviate micronutrient malnutrition of people world-wide.
Max ERC Funding
1 498 628 €
Duration
Start date: 2019-03-01, End date: 2024-02-29
