Project acronym UV-B Perception
Project UV-B perception and signalling by the UVR8 photoreceptor
Researcher (PI) Roman Ulm
Host Institution (HI) UNIVERSITE DE GENEVE
Call Details Starting Grant (StG), LS1, ERC-2012-StG_20111109
Summary Ultraviolet-B (UV-B) is a key environmental signal that is specifically perceived by plants and promotes UV acclimation and survival in sunlight. We discovered recently that the Arabidopsis UVR8 protein is absolutely required for UV-B acclimation and functions as the major UV-B photoreceptor in plants: UVR8 dimer perception of UV-B photons leads to monomerization and direct interaction with the E3 ubiquitin ligase COP1, the central regulator of light signalling. We proposed that the initial UV-B perception step by the UVR8 photoreceptor involves the aromatic amino acid tryptophan as a chromophore. The UVR8 protein contains 14 tryptophans, localized mostly at the top of the predicted UVR8 beta-propeller structure. This hydrophobic surface is probably the surface through which UVR8 dimerizes, generating a tryptophan-rich “interphase” between the two monomers. Although it is clear from our combined genetic, physiological, molecular and biochemical data that UVR8 functions as the long-sought-after UV-B photoreceptor in plants, the mechanism of UV-B absorption and the immediate impact on the UVR8 protein and its interactors remains elusive. We would like to address this current major gap in photobiology in frame of the ERC project “UV-B Perception”. The proposed project will provide mechanistic insights into this newly discovered perception mechanism and photoreceptor pathway, which is of utmost importance for the survival of plants.
Summary
Ultraviolet-B (UV-B) is a key environmental signal that is specifically perceived by plants and promotes UV acclimation and survival in sunlight. We discovered recently that the Arabidopsis UVR8 protein is absolutely required for UV-B acclimation and functions as the major UV-B photoreceptor in plants: UVR8 dimer perception of UV-B photons leads to monomerization and direct interaction with the E3 ubiquitin ligase COP1, the central regulator of light signalling. We proposed that the initial UV-B perception step by the UVR8 photoreceptor involves the aromatic amino acid tryptophan as a chromophore. The UVR8 protein contains 14 tryptophans, localized mostly at the top of the predicted UVR8 beta-propeller structure. This hydrophobic surface is probably the surface through which UVR8 dimerizes, generating a tryptophan-rich “interphase” between the two monomers. Although it is clear from our combined genetic, physiological, molecular and biochemical data that UVR8 functions as the long-sought-after UV-B photoreceptor in plants, the mechanism of UV-B absorption and the immediate impact on the UVR8 protein and its interactors remains elusive. We would like to address this current major gap in photobiology in frame of the ERC project “UV-B Perception”. The proposed project will provide mechanistic insights into this newly discovered perception mechanism and photoreceptor pathway, which is of utmost importance for the survival of plants.
Max ERC Funding
1 498 579 €
Duration
Start date: 2012-12-01, End date: 2017-11-30
Project acronym V-RNA
Project Two facets of viral RNA: mechanistic studies of transcription and replication by influenza-like viral polymerases and detection by the innate immune system
Researcher (PI) Stephen Anthony Cusack
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Call Details Advanced Grant (AdG), LS1, ERC-2012-ADG_20120314
Summary RNA viruses infect cells to replicate and repackage their genomes in progeny virions. In response, the cellular innate immune system detects viral RNA and triggers powerful anti-viral countermeasures. This proposal aims to elucidate atomic resolution molecular mechanisms associated with these conflicting interests, and will address the following questions: firstly, how do RNA polymerases of segmented, negative sense, single-stranded RNA viruses such as influenza and bunyaviruses transcribe and replicate viral RNA and secondly, how do RIG-I like helicases, intracellular, innate immune, pattern recognition receptors, selectively detect RNA only of viral origin, thus triggering interferon production and induction of the anti-viral state? A third, more exploratory part of the proposal will use proteomics analysis to identify all host factors that are bound to viral mRNAs in influenza virus infected cells. The interdisciplinary project will combine state-of-the-art structural biology with cell-based functional assays and global analysis. Results will advance fundamental understanding of polymerases and helicases, both complex RNA-dependent molecular machines, give new insight into the regulation of innate immune receptor activation and signalling, and shed new light on RNA metabolism in the perturbed environment of the infected cell. They will also impact virology and public health by bringing new knowledge on RNA virus-host interactions, virus evolution and inter-species transmission. More pragmatically the project will boost structure-based anti-viral drug development targeting serious and/or emerging human pathogens such as influenza A, which poses the perennial threat of a devastating pandemic, and the many disease causing bunyaviruses, which in a globally warming world could spread unpredictably. The V-RNA project thus forms a coherent whole covering important protagonists in the virus-versus-host-versus-virus molecular warfare centered around viral RNA.
Summary
RNA viruses infect cells to replicate and repackage their genomes in progeny virions. In response, the cellular innate immune system detects viral RNA and triggers powerful anti-viral countermeasures. This proposal aims to elucidate atomic resolution molecular mechanisms associated with these conflicting interests, and will address the following questions: firstly, how do RNA polymerases of segmented, negative sense, single-stranded RNA viruses such as influenza and bunyaviruses transcribe and replicate viral RNA and secondly, how do RIG-I like helicases, intracellular, innate immune, pattern recognition receptors, selectively detect RNA only of viral origin, thus triggering interferon production and induction of the anti-viral state? A third, more exploratory part of the proposal will use proteomics analysis to identify all host factors that are bound to viral mRNAs in influenza virus infected cells. The interdisciplinary project will combine state-of-the-art structural biology with cell-based functional assays and global analysis. Results will advance fundamental understanding of polymerases and helicases, both complex RNA-dependent molecular machines, give new insight into the regulation of innate immune receptor activation and signalling, and shed new light on RNA metabolism in the perturbed environment of the infected cell. They will also impact virology and public health by bringing new knowledge on RNA virus-host interactions, virus evolution and inter-species transmission. More pragmatically the project will boost structure-based anti-viral drug development targeting serious and/or emerging human pathogens such as influenza A, which poses the perennial threat of a devastating pandemic, and the many disease causing bunyaviruses, which in a globally warming world could spread unpredictably. The V-RNA project thus forms a coherent whole covering important protagonists in the virus-versus-host-versus-virus molecular warfare centered around viral RNA.
Max ERC Funding
2 371 934 €
Duration
Start date: 2013-05-01, End date: 2018-04-30
Project acronym VIDOCK
Project 2D Conformal mapping of protein surfaces: applications to VIsualization and DOCKing software
Researcher (PI) Matthieu Olivier Montes
Host Institution (HI) CONSERVATOIRE NATIONAL DES ARTS ET METIERS
Call Details Starting Grant (StG), LS1, ERC-2014-STG
Summary The goals of structural biology include developing a comprehensive understanding of the molecular shapes and forms embraced by biological macromolecules and extending this knowledge to understand how different molecular architectures are used to perform the chemical reactions that are central to life.
Since the first resolution of protein structures by X-ray crystallography and NMR, structural biology seeks to provide this picture of biological phenomena at the molecular and atomic level by analyzing 3D structures.
In the present proposal, we propose to change this paradigm by changing the mode of representation of protein surfaces to 2D maps. That will open new avenues for 1. the development of innovative high-throughput computation of protein interactions and relationships and 2. the emergence of new forms of visualization and analysis of protein structures and properties. We will apply this powerful tool of conformal mapping to structural biology by representing protein surfaces that are complex 3D surfaces in 2D conformal maps that we will call positive conformal maps. We will extend this representation by also generating the 2D conformal maps of the negatives of the 3D surface of the proteins. These positive and negative 2D conformal maps of the surface of proteins will constitute a new representation of the protein surfaces that will be the basis for innovative high-throughput and/or interactive simulation methods, visualization methods and more generally that will give an other insight on the structure of proteins.
The major impact of this proposal lies in the fact that it will at last open the gates of the long awaited proteome docking. Using a simplified representation of protein surfaces will allow to perform faster complete cross docking calculations and create a new classification of the protein structures based on their surficial similarity.
Summary
The goals of structural biology include developing a comprehensive understanding of the molecular shapes and forms embraced by biological macromolecules and extending this knowledge to understand how different molecular architectures are used to perform the chemical reactions that are central to life.
Since the first resolution of protein structures by X-ray crystallography and NMR, structural biology seeks to provide this picture of biological phenomena at the molecular and atomic level by analyzing 3D structures.
In the present proposal, we propose to change this paradigm by changing the mode of representation of protein surfaces to 2D maps. That will open new avenues for 1. the development of innovative high-throughput computation of protein interactions and relationships and 2. the emergence of new forms of visualization and analysis of protein structures and properties. We will apply this powerful tool of conformal mapping to structural biology by representing protein surfaces that are complex 3D surfaces in 2D conformal maps that we will call positive conformal maps. We will extend this representation by also generating the 2D conformal maps of the negatives of the 3D surface of the proteins. These positive and negative 2D conformal maps of the surface of proteins will constitute a new representation of the protein surfaces that will be the basis for innovative high-throughput and/or interactive simulation methods, visualization methods and more generally that will give an other insight on the structure of proteins.
The major impact of this proposal lies in the fact that it will at last open the gates of the long awaited proteome docking. Using a simplified representation of protein surfaces will allow to perform faster complete cross docking calculations and create a new classification of the protein structures based on their surficial similarity.
Max ERC Funding
1 498 791 €
Duration
Start date: 2015-07-01, End date: 2021-06-30
Project acronym VIREVOL
Project Cells and giant viruses: a win-win co-evolution
Researcher (PI) Chantal ABERGEL
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Advanced Grant (AdG), LS1, ERC-2018-ADG
Summary The discovery of Mimivirus, the first icosahedral virus visible by light microscopy, was followed by the characterization of many other relatives. Its aquatic relative Megavirus chilensis, has a 1.2 Mb genome and encodes more than 1000 proteins, 2/3 unique to the Mimiviridae. Their infectious cycle is cytoplasmic. During the last 10 years, my laboratory discovered three other giant virus families: -the pandoraviridae, with their unique amphora-shaped 1µm long virion morphologies, genome sizes reaching 3Mb and encoding thousands of proteins, most of which without homologues in the cellular or the viral world – the mollivirus, which was isolated from a 30,000 years old Siberian permafrost sample, presents common features with the pandoraviruses. They share 60 unique genes and the roughly spherical (0.6µm) mollivirions present an external tegument resembling the pandoravirions. Both viruses have an early nuclear phase – the pithovirus, despite its amphora-shaped virions, has a fully cytoplasmic cycle. Our work raised questions on the origin of these intriguing viral families and their position in the tree of life. My project is unique as it will address the coevolution of these viruses and their amoebal hosts by focusing on specific features of the virions in two overall aims. 1) Promising preliminary results led us to hypothesize that a progressive transition from the rigid icosahedral virions to the more plastic amphora-shaped particles was made possible through hijacking of the host cellulose synthesis pathway by the ancestor of pandoraviruses. 2) The icosahedral mimivirus package its genome in a complex rod-shaped structure. My team will investigate this structure to unveil possible evolutionary links with the genome packaging systems in the cellular world. We will characterize the machinery responsible for such organization. These two high-risk/high-gain aims will continue to revisit the concept of virus and their evolutionary trajectory in the living world.
Summary
The discovery of Mimivirus, the first icosahedral virus visible by light microscopy, was followed by the characterization of many other relatives. Its aquatic relative Megavirus chilensis, has a 1.2 Mb genome and encodes more than 1000 proteins, 2/3 unique to the Mimiviridae. Their infectious cycle is cytoplasmic. During the last 10 years, my laboratory discovered three other giant virus families: -the pandoraviridae, with their unique amphora-shaped 1µm long virion morphologies, genome sizes reaching 3Mb and encoding thousands of proteins, most of which without homologues in the cellular or the viral world – the mollivirus, which was isolated from a 30,000 years old Siberian permafrost sample, presents common features with the pandoraviruses. They share 60 unique genes and the roughly spherical (0.6µm) mollivirions present an external tegument resembling the pandoravirions. Both viruses have an early nuclear phase – the pithovirus, despite its amphora-shaped virions, has a fully cytoplasmic cycle. Our work raised questions on the origin of these intriguing viral families and their position in the tree of life. My project is unique as it will address the coevolution of these viruses and their amoebal hosts by focusing on specific features of the virions in two overall aims. 1) Promising preliminary results led us to hypothesize that a progressive transition from the rigid icosahedral virions to the more plastic amphora-shaped particles was made possible through hijacking of the host cellulose synthesis pathway by the ancestor of pandoraviruses. 2) The icosahedral mimivirus package its genome in a complex rod-shaped structure. My team will investigate this structure to unveil possible evolutionary links with the genome packaging systems in the cellular world. We will characterize the machinery responsible for such organization. These two high-risk/high-gain aims will continue to revisit the concept of virus and their evolutionary trajectory in the living world.
Max ERC Funding
2 246 453 €
Duration
Start date: 2019-10-01, End date: 2024-09-30
Project acronym VisTrans
Project Visualising transport dynamics of transmembrane pumps
Researcher (PI) Bonaventura LUISI
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS1, ERC-2016-ADG
Summary The project will investigate multi-component molecular machines that drive substrates across the cell envelope of bacteria. Some of the machines pump antibiotics or toxins, and so contribute to drug resistance and virulence in pathogenic strains. Questions that will be addressed include what the molecular pumps look like, how they are assembled and regulated, how they capture and translocate substrates, and the stereochemical basis for the cooperative switching of substrate-binding states. Molecular pumps that will be studied include tripartite systems driven by ATP hydrolysis, which play a central role in the efflux of macrolide antibiotics and secretion of toxins in Gram-negative bacteria, and those that use secondary transporters energized by electrochemical gradients. We will build upon our earlier observations to prepare a series of intermediates encompassing the key steps in the transport processes, to visualize tertiary and quaternary structural changes, the pathway of substrates in the efflux pumps, and the threading of toxin polypeptides through the constricted channel in the secretion assembly. The pumps and secretion systems cycle through intermediate states, and these will be studied at high resolution by cryoEM and crystallography to understand how the conformational states switch with strong cooperativity and avoid futile cycles that dissipate energy. Our work indicates that the activity of these transporters can be modulated by small peptides and potential co-factors, and we will address how these work. The project will build on our novel approach to engineer the pump assemblies that enables structural analysis at high resolution in isolation and in situ, and will be complemented with mechanistic analyses in vitro and in vivo. The project will deliver a comprehensive, structure-based description of the mechanism of drug efflux and protein translocation by transport machines and their regulation in diverse pathogenic bacteria.
Summary
The project will investigate multi-component molecular machines that drive substrates across the cell envelope of bacteria. Some of the machines pump antibiotics or toxins, and so contribute to drug resistance and virulence in pathogenic strains. Questions that will be addressed include what the molecular pumps look like, how they are assembled and regulated, how they capture and translocate substrates, and the stereochemical basis for the cooperative switching of substrate-binding states. Molecular pumps that will be studied include tripartite systems driven by ATP hydrolysis, which play a central role in the efflux of macrolide antibiotics and secretion of toxins in Gram-negative bacteria, and those that use secondary transporters energized by electrochemical gradients. We will build upon our earlier observations to prepare a series of intermediates encompassing the key steps in the transport processes, to visualize tertiary and quaternary structural changes, the pathway of substrates in the efflux pumps, and the threading of toxin polypeptides through the constricted channel in the secretion assembly. The pumps and secretion systems cycle through intermediate states, and these will be studied at high resolution by cryoEM and crystallography to understand how the conformational states switch with strong cooperativity and avoid futile cycles that dissipate energy. Our work indicates that the activity of these transporters can be modulated by small peptides and potential co-factors, and we will address how these work. The project will build on our novel approach to engineer the pump assemblies that enables structural analysis at high resolution in isolation and in situ, and will be complemented with mechanistic analyses in vitro and in vivo. The project will deliver a comprehensive, structure-based description of the mechanism of drug efflux and protein translocation by transport machines and their regulation in diverse pathogenic bacteria.
Max ERC Funding
2 208 619 €
Duration
Start date: 2017-09-01, End date: 2022-08-31
