Project acronym ANOBEST
Project Structure function and pharmacology of calcium-activated chloride channels: Anoctamins and Bestrophins
Researcher (PI) Raimund Dutzler
Host Institution (HI) University of Zurich
Country Switzerland
Call Details Advanced Grant (AdG), LS1, ERC-2013-ADG
Summary Calcium-activated chloride channels (CaCCs) play key roles in a range of physiological processes such as the control of membrane excitability, photoreception and epithelial secretion. Although the importance of these channels has been recognized for more than 30 years their molecular identity remained obscure. The recent discovery of two protein families encoding for CaCCs, Anoctamins and Bestrophins, was a scientific breakthrough that has provided first insight into two novel ion channel architectures. Within this proposal we aim to determine the first high resolution structures of members of both families and study their functional behavior by an interdisciplinary approach combining biochemistry, X-ray crystallography and electrophysiology. The structural investigation of eukaryotic membrane proteins is extremely challenging and will require us to investigate large numbers of candidates to single out family members with superior biochemical properties. During the last year we have made large progress in this direction. By screening numerous eukaryotic Anoctamins and prokaryotic Bestrophins we have identified well-behaved proteins for both families, which were successfully scaled-up and purified. Additional family members will be identified within the course of the project. For these stable proteins we plan to grow crystals diffracting to high resolution and to proceed with structure determination. With first structural information in hand we will perform detailed functional studies using electrophysiology and complementary biophysical techniques to gain mechanistic insight into ion permeation and gating. As the pharmacology of both families is still in its infancy we will in later stages also engage in the identification and characterization of inhibitors and activators of Anoctamins and Bestrophins to open up a field that may ultimately lead to the discovery of novel therapeutic strategies targeting calcium-activated chloride channels.
Summary
Calcium-activated chloride channels (CaCCs) play key roles in a range of physiological processes such as the control of membrane excitability, photoreception and epithelial secretion. Although the importance of these channels has been recognized for more than 30 years their molecular identity remained obscure. The recent discovery of two protein families encoding for CaCCs, Anoctamins and Bestrophins, was a scientific breakthrough that has provided first insight into two novel ion channel architectures. Within this proposal we aim to determine the first high resolution structures of members of both families and study their functional behavior by an interdisciplinary approach combining biochemistry, X-ray crystallography and electrophysiology. The structural investigation of eukaryotic membrane proteins is extremely challenging and will require us to investigate large numbers of candidates to single out family members with superior biochemical properties. During the last year we have made large progress in this direction. By screening numerous eukaryotic Anoctamins and prokaryotic Bestrophins we have identified well-behaved proteins for both families, which were successfully scaled-up and purified. Additional family members will be identified within the course of the project. For these stable proteins we plan to grow crystals diffracting to high resolution and to proceed with structure determination. With first structural information in hand we will perform detailed functional studies using electrophysiology and complementary biophysical techniques to gain mechanistic insight into ion permeation and gating. As the pharmacology of both families is still in its infancy we will in later stages also engage in the identification and characterization of inhibitors and activators of Anoctamins and Bestrophins to open up a field that may ultimately lead to the discovery of novel therapeutic strategies targeting calcium-activated chloride channels.
Max ERC Funding
2 176 000 €
Duration
Start date: 2014-02-01, End date: 2020-01-31
Project acronym BIOCARB
Project Carbonate Biomineralization in the Marine Environment: Paleo-climate proxies and the origin of vital effects
Researcher (PI) Anders Meibom
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Country Switzerland
Call Details Advanced Grant (AdG), PE10, ERC-2009-AdG
Summary This interdisciplinary proposal has the objective to greatly enhance our understanding of fundamental biomineralization processes involved in the formation of calcium carbonates by marine organisms, such as corals, foraminifera and bivalves, in order to better understand vital effects. This is essential to the application of these carbonates as proxies for global (paleo-) environmental change. The core of the proposal is an experimental capability that I have pioneered during 2008: Dynamic stable isotopic labeling during formation of carbonate skeletons, tests, and shells, combined with NanoSIMS imaging. The NanoSIMS ion microprobe is a state-of-the-art analytical technology that allows precise elemental and isotopic imaging with a spatial resolution of ~100 nanometers. NanoSIMS imaging of the isotopic label(s) in the resulting biocarbonates and in associated cell-structures will be used to uncover cellular-level transport processes, timescales of formation of different biocarbonate components, as well as trace-elemental and isotopic fractionations. This will uncover the origin of vital effects. With this proposal, I establish a new scientific frontier and guarantee European leadership. The technical and scientific developments resulting from this work are broadly applicable and will radically change scientific ideas about marine carbonate biomineralization and compositional vital effects.
Summary
This interdisciplinary proposal has the objective to greatly enhance our understanding of fundamental biomineralization processes involved in the formation of calcium carbonates by marine organisms, such as corals, foraminifera and bivalves, in order to better understand vital effects. This is essential to the application of these carbonates as proxies for global (paleo-) environmental change. The core of the proposal is an experimental capability that I have pioneered during 2008: Dynamic stable isotopic labeling during formation of carbonate skeletons, tests, and shells, combined with NanoSIMS imaging. The NanoSIMS ion microprobe is a state-of-the-art analytical technology that allows precise elemental and isotopic imaging with a spatial resolution of ~100 nanometers. NanoSIMS imaging of the isotopic label(s) in the resulting biocarbonates and in associated cell-structures will be used to uncover cellular-level transport processes, timescales of formation of different biocarbonate components, as well as trace-elemental and isotopic fractionations. This will uncover the origin of vital effects. With this proposal, I establish a new scientific frontier and guarantee European leadership. The technical and scientific developments resulting from this work are broadly applicable and will radically change scientific ideas about marine carbonate biomineralization and compositional vital effects.
Max ERC Funding
2 182 000 €
Duration
Start date: 2010-07-01, End date: 2015-06-30
Project acronym CFRFSS
Project Chromatin Fiber and Remodeling Factor Structural Studies
Researcher (PI) Timothy John Richmond
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Country Switzerland
Call Details Advanced Grant (AdG), LS1, ERC-2012-ADG_20120314
Summary "DNA in higher organisms is organized in a nucleoprotein complex called chromatin. The structure of chromatin is responsible for compacting DNA to fit within the nucleus and for governing its access in nuclear processes. Epigenetic information is encoded chiefly via chromatin modifications. Readout of the genetic code depends on chromatin remodeling, a process actively altering chromatin structure. An understanding of the hierarchical structure of chromatin and of structurally based, remodeling mechanisms will have enormous impact for developments in medicine.
Following our high resolution structure of the nucleosome core particle, the fundamental repeating unit of chromatin, we have endeavored to determine the structure of the chromatin fiber. We showed with our X-ray structure of a tetranucleosome how nucleosomes could be organized in the fiber. Further progress has been limited by structural polymorphism and crystal disorder, but new evidence on the in vivo spacing of nucleosomes in chromatin should stimulate more advances. Part A of this application describes how we would apply these new findings to our cryo-electron microscopy study of the chromatin fiber and to our crystallographic study of a tetranucleosome containing linker histone.
Recently, my laboratory succeeded in providing the first structurally based mechanism for nucleosome spacing by a chromatin remodeling factor. We combined the X-ray structure of ISW1a(ATPase) bound to DNA with cryo-EM structures of the factor bound to two different nucleosomes to build a model showing how this remodeler uses a dinucleosome, not a mononucleosome, as its substrate. Our results from a functional assay using ISW1a further justified this model. Part B of this application describes how we would proceed to the relevant cryo-EM and X-ray structures incorporating dinucleosomes. Our recombinant ISW1a allows us to study in addition the interaction of the ATPase domain with nucleosome substrates."
Summary
"DNA in higher organisms is organized in a nucleoprotein complex called chromatin. The structure of chromatin is responsible for compacting DNA to fit within the nucleus and for governing its access in nuclear processes. Epigenetic information is encoded chiefly via chromatin modifications. Readout of the genetic code depends on chromatin remodeling, a process actively altering chromatin structure. An understanding of the hierarchical structure of chromatin and of structurally based, remodeling mechanisms will have enormous impact for developments in medicine.
Following our high resolution structure of the nucleosome core particle, the fundamental repeating unit of chromatin, we have endeavored to determine the structure of the chromatin fiber. We showed with our X-ray structure of a tetranucleosome how nucleosomes could be organized in the fiber. Further progress has been limited by structural polymorphism and crystal disorder, but new evidence on the in vivo spacing of nucleosomes in chromatin should stimulate more advances. Part A of this application describes how we would apply these new findings to our cryo-electron microscopy study of the chromatin fiber and to our crystallographic study of a tetranucleosome containing linker histone.
Recently, my laboratory succeeded in providing the first structurally based mechanism for nucleosome spacing by a chromatin remodeling factor. We combined the X-ray structure of ISW1a(ATPase) bound to DNA with cryo-EM structures of the factor bound to two different nucleosomes to build a model showing how this remodeler uses a dinucleosome, not a mononucleosome, as its substrate. Our results from a functional assay using ISW1a further justified this model. Part B of this application describes how we would proceed to the relevant cryo-EM and X-ray structures incorporating dinucleosomes. Our recombinant ISW1a allows us to study in addition the interaction of the ATPase domain with nucleosome substrates."
Max ERC Funding
2 500 000 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym CHLIP
Project "Understanding Halogenated Lipids: Synthesis, Mode of Action, Structural Studies, and Applications"
Researcher (PI) Erick Moran Carreira
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Country Switzerland
Call Details Advanced Grant (AdG), PE5, ERC-2012-ADG_20120216
Summary "Among the various toxins isolated, the chlorosulfolipids are particularly intriguing because of their structural and stereochemical complexity. The mechanism of biological activity remains unknown. The lack of availability of the natural products has impaired more in-depth studies aimed at pharmacological, biological, and chemical characterization for proper evaluation of the risk for human health and their role in nature. The proposal takes as its basis this unusual class of natural products and delineates a multifaceted program of inquiry involving: (1) structural characterization of the most complex chlorosulfolipid isolated to date, (2) conformational studies in solution of chlorinated lipids, (3) synthesis and study of brominated lipid analogs, (4) development of analytical methods for detection of these toxins in the environment, (5) the discovery and development of reagents and catalysts for asymmetric chlorination of olefins, (6) examination of lipid conformation in constrained media, (7) examination of the mechanism of anchimeric assistance by chlorides, and (8) applications to drug discovery."
Summary
"Among the various toxins isolated, the chlorosulfolipids are particularly intriguing because of their structural and stereochemical complexity. The mechanism of biological activity remains unknown. The lack of availability of the natural products has impaired more in-depth studies aimed at pharmacological, biological, and chemical characterization for proper evaluation of the risk for human health and their role in nature. The proposal takes as its basis this unusual class of natural products and delineates a multifaceted program of inquiry involving: (1) structural characterization of the most complex chlorosulfolipid isolated to date, (2) conformational studies in solution of chlorinated lipids, (3) synthesis and study of brominated lipid analogs, (4) development of analytical methods for detection of these toxins in the environment, (5) the discovery and development of reagents and catalysts for asymmetric chlorination of olefins, (6) examination of lipid conformation in constrained media, (7) examination of the mechanism of anchimeric assistance by chlorides, and (8) applications to drug discovery."
Max ERC Funding
2 233 240 €
Duration
Start date: 2013-03-01, End date: 2018-02-28
Project acronym CHROMARRANGE
Project Programmed and unprogrammed genomic rearrangements during the evolution of yeast species
Researcher (PI) Kenneth Henry Wolfe
Host Institution (HI) UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN
Country Ireland
Call Details Advanced Grant (AdG), LS2, ERC-2010-AdG_20100317
Summary By detailed evolutionary comparisons among multiple sequenced yeast genomes, we have identified several unusual regions where our preliminary evidence suggests that previously unknown molecular biology phenomena, involving rearrangement of genomic DNA, are occurring. I now propose to use a combination of dry-lab and wet-lab experimental approaches to characterize these regions and phenomena further. One region is a 24-kb section of chromosome XIV that appears to undergo recurrent 'flip/flop' inversion between two isomers at a fairly high rate in five species as diverse as Saccharomyces cerevisiae and Naumovia castellii, leading to a 1:1 ratio of the two isomers in each species. We hypothesize that this region is the site of a programmed DNA rearrangement analogous to mating-type switching. We have also identified two new genes related to the mating-type switching endonuclease HO, but different from it, that are potentially involved in rearrangement processes though not necessarily the inversion described above. We will determine the sites of action of these endonucleases. Separately, we have found evidence for a process of recurrent deletion of DNA from regions flanking the mating-type (MAT) locus in all yeast species that are descended from the whole-genome duplication (WGD) event, causing continual transpositions of genes from beside MAT to other locations in the genome. In related computational work, we propose to investigate an hypothesis that evolutionary loss of the MATa2 transcriptional activator may have been the cause of the WGD event.
Summary
By detailed evolutionary comparisons among multiple sequenced yeast genomes, we have identified several unusual regions where our preliminary evidence suggests that previously unknown molecular biology phenomena, involving rearrangement of genomic DNA, are occurring. I now propose to use a combination of dry-lab and wet-lab experimental approaches to characterize these regions and phenomena further. One region is a 24-kb section of chromosome XIV that appears to undergo recurrent 'flip/flop' inversion between two isomers at a fairly high rate in five species as diverse as Saccharomyces cerevisiae and Naumovia castellii, leading to a 1:1 ratio of the two isomers in each species. We hypothesize that this region is the site of a programmed DNA rearrangement analogous to mating-type switching. We have also identified two new genes related to the mating-type switching endonuclease HO, but different from it, that are potentially involved in rearrangement processes though not necessarily the inversion described above. We will determine the sites of action of these endonucleases. Separately, we have found evidence for a process of recurrent deletion of DNA from regions flanking the mating-type (MAT) locus in all yeast species that are descended from the whole-genome duplication (WGD) event, causing continual transpositions of genes from beside MAT to other locations in the genome. In related computational work, we propose to investigate an hypothesis that evolutionary loss of the MATa2 transcriptional activator may have been the cause of the WGD event.
Max ERC Funding
1 516 960 €
Duration
Start date: 2011-06-01, End date: 2016-05-31
Project acronym CODEKILLER
Project Killer plasmids as drivers of genetic code changes during yeast evolution
Researcher (PI) Kenneth WOLFE
Host Institution (HI) UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN
Country Ireland
Call Details Advanced Grant (AdG), LS8, ERC-2017-ADG
Summary The genetic code was established at a very early stage during the evolution of life on Earth and is nearly universal. In eukaryotic nuclear genes, the only known examples of a sense codon that underwent an evolutionary change of meaning, from one amino acid to another, occur in yeast species. The codon CUG is translated as Leu in the universal genetic code, but it has long been known to be translated as Ser in some Candida species. In recent work, we discovered that this switch is one of three parallel reassignments of CUG that occurred in three closely related clades of yeasts. CUG was reassigned once from Leu to Ala, and twice from Leu to Ser, in three separate events. The meaning of sense codons in the nuclear genetic code has otherwise remained completely stable during all of eukaryotic evolution, so why was CUG so unstable in yeasts? CODEKILLER will test a radical new hypothesis that the genetic code changes were caused by a killer toxin that specifically attacked the tRNA that translated CUG as Leu. The hypothesis implies that the reassignments of CUG were not driven by selection in favor of their effects on the proteome, as commonly assumed, but by selection against the existence of a particular tRNA. As well as searching for this killer toxin, we will study the detailed mechanism of genetic code change by engineering a reversal of a CUG-Ser species back to CUG-Leu translation, and investigate translation in some species that naturally contain both tRNA-Leu and tRNA-Ser molecules capable of decoding CUG.
Summary
The genetic code was established at a very early stage during the evolution of life on Earth and is nearly universal. In eukaryotic nuclear genes, the only known examples of a sense codon that underwent an evolutionary change of meaning, from one amino acid to another, occur in yeast species. The codon CUG is translated as Leu in the universal genetic code, but it has long been known to be translated as Ser in some Candida species. In recent work, we discovered that this switch is one of three parallel reassignments of CUG that occurred in three closely related clades of yeasts. CUG was reassigned once from Leu to Ala, and twice from Leu to Ser, in three separate events. The meaning of sense codons in the nuclear genetic code has otherwise remained completely stable during all of eukaryotic evolution, so why was CUG so unstable in yeasts? CODEKILLER will test a radical new hypothesis that the genetic code changes were caused by a killer toxin that specifically attacked the tRNA that translated CUG as Leu. The hypothesis implies that the reassignments of CUG were not driven by selection in favor of their effects on the proteome, as commonly assumed, but by selection against the existence of a particular tRNA. As well as searching for this killer toxin, we will study the detailed mechanism of genetic code change by engineering a reversal of a CUG-Ser species back to CUG-Leu translation, and investigate translation in some species that naturally contain both tRNA-Leu and tRNA-Ser molecules capable of decoding CUG.
Max ERC Funding
2 368 356 €
Duration
Start date: 2018-10-01, End date: 2023-09-30
Project acronym COGNET
Project Cognitive Networks for Intelligent Materials and Devices
Researcher (PI) John Boland
Host Institution (HI) THE PROVOST, FELLOWS, FOUNDATION SCHOLARS & THE OTHER MEMBERS OF BOARD OF THE COLLEGE OF THE HOLY & UNDIVIDED TRINITY OF QUEEN ELIZABETH NEAR DUBLIN
Country Ireland
Call Details Advanced Grant (AdG), PE5, ERC-2012-ADG_20120216
Summary "COGnitive NETwork (COGNET) is a new technology platform for materials, sensor and device design that exploits unique and hitherto unrecognised properties of random nanowire (NW) networks. These networks—comprised of metallic or semiconducting NWs connected to each other via junctions with controllably random property distributions—lead to new and unexpected levels of connectivity that are inherently scale dependent, creating opportunities for entirely new kinds of self-organised materials and devices. We propose to establish the ground rules for manipulating connectivity in NW networks. By choosing appropriate NWs and incorporating junctions with the approprate properties COGNET will enable the fabrication of (i) intelligent materials, (ii) neural networks and (iii) memory devices. Sequenced voltage pulse and back-gating techniques will in turn address and manipulate specific junctions or sets of junctions to demonstrate even higher density memory and in the case of neural networks, the possibility synaptic plasticity and self-learning."
Summary
"COGnitive NETwork (COGNET) is a new technology platform for materials, sensor and device design that exploits unique and hitherto unrecognised properties of random nanowire (NW) networks. These networks—comprised of metallic or semiconducting NWs connected to each other via junctions with controllably random property distributions—lead to new and unexpected levels of connectivity that are inherently scale dependent, creating opportunities for entirely new kinds of self-organised materials and devices. We propose to establish the ground rules for manipulating connectivity in NW networks. By choosing appropriate NWs and incorporating junctions with the approprate properties COGNET will enable the fabrication of (i) intelligent materials, (ii) neural networks and (iii) memory devices. Sequenced voltage pulse and back-gating techniques will in turn address and manipulate specific junctions or sets of junctions to demonstrate even higher density memory and in the case of neural networks, the possibility synaptic plasticity and self-learning."
Max ERC Funding
2 497 125 €
Duration
Start date: 2013-06-01, End date: 2018-05-31
Project acronym CROSSINGSCALES
Project Reverse Scale-Crossing Effects In Biology
Researcher (PI) Lucas PELKMANS
Host Institution (HI) UNIVERSITAT ZURICH
Country Switzerland
Call Details Advanced Grant (AdG), LS2, ERC-2019-ADG
Summary The central dogma in biology often invokes a bottom-up picture of life. However, at different biological scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components from which these new properties emerge. These top-down or reverse scale-crossing effects must be taken into account in order to make predictions about spatiotemporally controlled single-cell fates, activities, levels of gene expression, or the functional outcome of cellular signalling. They can stem from the multicellular, the cellular, and the intracellular scale, and can be quantified using multiscale and multiplexed RNA and protein state imaging in combination with computer vision and data-driven modelling. The ability to comprehensively map these reverse causal effects across multiple scales has the potential to revolutionize most, if not all domains of biology and medicine. In this project, we will establish the importance of reverse causal effects in human induced pluripotent stem cells and early D. rerio embryos. To achieve this, we will develop a quantitative imaging method beyond the diffraction limit of light without compromising scalability in temporal and spatial dimensions. We will also develop a method that achieves scalable, transcriptome-wide image-based multiplexing of mRNA transcripts, and we will extend our computer vision approaches to higher resolution and to three spatial dimensions. These methods will be systematically applied to stem cell collectives grown in 2D and 3D, as well as to early embryos, achieving comprehensive quantification of nuclear and chromatin states, gene expression, subcellular organization, cellular states, and tissue-scale organization across millions of individual cells within the same dataset. These datasets will be used to quantify how, at different scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components
Summary
The central dogma in biology often invokes a bottom-up picture of life. However, at different biological scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components from which these new properties emerge. These top-down or reverse scale-crossing effects must be taken into account in order to make predictions about spatiotemporally controlled single-cell fates, activities, levels of gene expression, or the functional outcome of cellular signalling. They can stem from the multicellular, the cellular, and the intracellular scale, and can be quantified using multiscale and multiplexed RNA and protein state imaging in combination with computer vision and data-driven modelling. The ability to comprehensively map these reverse causal effects across multiple scales has the potential to revolutionize most, if not all domains of biology and medicine. In this project, we will establish the importance of reverse causal effects in human induced pluripotent stem cells and early D. rerio embryos. To achieve this, we will develop a quantitative imaging method beyond the diffraction limit of light without compromising scalability in temporal and spatial dimensions. We will also develop a method that achieves scalable, transcriptome-wide image-based multiplexing of mRNA transcripts, and we will extend our computer vision approaches to higher resolution and to three spatial dimensions. These methods will be systematically applied to stem cell collectives grown in 2D and 3D, as well as to early embryos, achieving comprehensive quantification of nuclear and chromatin states, gene expression, subcellular organization, cellular states, and tissue-scale organization across millions of individual cells within the same dataset. These datasets will be used to quantify how, at different scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components
Max ERC Funding
2 411 075 €
Duration
Start date: 2020-09-01, End date: 2025-08-31
Project acronym CsnCRL
Project The molecular basis of CULLIN E3 ligase regulation by the COP9 signalosome
Researcher (PI) Nicolas Thoma
Host Institution (HI) FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH FONDATION
Country Switzerland
Call Details Advanced Grant (AdG), LS1, ERC-2014-ADG
Summary Specificity in the ubiquitin-proteasome system is largely conferred by ubiquitin E3 ligases (E3s). Cullin-RING ligases (CRLs), constituting ~30% of all E3s in humans, mediate the ubiquitination of ~20% of the proteins degraded by the proteasome. CRLs are divided into seven families based on their cullin constituent. Each cullin binds a RING domain protein, and a vast repertoire of adaptor/substrate receptor modules, collectively creating more than 200 distinct CRLs. All CRLs are regulated by the COP9 signalosome (CSN), an eight-protein isopeptidase that removes the covalently attached activator, NEDD8, from the cullin. Independent of NEDD8 cleavage, CSN forms protective complexes with CRLs, which prevents destructive auto-ubiquitination.
The integrity of the CSN-CRL system is crucially important for the normal cell physiology. Based on our previous work on CRL structures (Fischer, et al., Nature 2014; Fischer, et al., Cell 2011) and that of isolated CSN (Lingaraju et al., Nature 2014), We now intend to provide the underlying molecular mechanism of CRL regulation by CSN. Structural insights at atomic resolution, combined with in vitro and in vivo functional studies are designed to reveal (i) how the signalosome deneddylates and maintains the bound ligases in an inactive state, (ii) how the multiple CSN subunits bind to structurally diverse CRLs, and (iii) how CSN is itself subject to regulation by post-translational modifications or additional further factors.
The ERC funding would allow my lab to pursue an ambitious interdisciplinary approach combining X-ray crystallography, cryo-electron microscopy, biochemistry and cell biology. This is expected to provide a unique molecular understanding of CSN action. Beyond ubiquitination, insight into this >13- subunit CSN-CRL assembly will allow examining general principles of multi-subunit complex action and reveal how the numerous, often essential, subunits contribute to complex function.
Summary
Specificity in the ubiquitin-proteasome system is largely conferred by ubiquitin E3 ligases (E3s). Cullin-RING ligases (CRLs), constituting ~30% of all E3s in humans, mediate the ubiquitination of ~20% of the proteins degraded by the proteasome. CRLs are divided into seven families based on their cullin constituent. Each cullin binds a RING domain protein, and a vast repertoire of adaptor/substrate receptor modules, collectively creating more than 200 distinct CRLs. All CRLs are regulated by the COP9 signalosome (CSN), an eight-protein isopeptidase that removes the covalently attached activator, NEDD8, from the cullin. Independent of NEDD8 cleavage, CSN forms protective complexes with CRLs, which prevents destructive auto-ubiquitination.
The integrity of the CSN-CRL system is crucially important for the normal cell physiology. Based on our previous work on CRL structures (Fischer, et al., Nature 2014; Fischer, et al., Cell 2011) and that of isolated CSN (Lingaraju et al., Nature 2014), We now intend to provide the underlying molecular mechanism of CRL regulation by CSN. Structural insights at atomic resolution, combined with in vitro and in vivo functional studies are designed to reveal (i) how the signalosome deneddylates and maintains the bound ligases in an inactive state, (ii) how the multiple CSN subunits bind to structurally diverse CRLs, and (iii) how CSN is itself subject to regulation by post-translational modifications or additional further factors.
The ERC funding would allow my lab to pursue an ambitious interdisciplinary approach combining X-ray crystallography, cryo-electron microscopy, biochemistry and cell biology. This is expected to provide a unique molecular understanding of CSN action. Beyond ubiquitination, insight into this >13- subunit CSN-CRL assembly will allow examining general principles of multi-subunit complex action and reveal how the numerous, often essential, subunits contribute to complex function.
Max ERC Funding
2 200 677 €
Duration
Start date: 2016-01-01, End date: 2021-02-28
Project acronym deepSLice
Project Deciphering the greenhouse gas record in deepest ice using continuous sublimation extraction / laser spectrometry
Researcher (PI) Hubertus Fischer
Host Institution (HI) UNIVERSITAET BERN
Country Switzerland
Call Details Advanced Grant (AdG), PE10, ERC-2014-ADG
Summary The recent anthropogenic global warming makes a detailed understanding of coupling processes between climate and biogeochemical cycles of pressing importance. The atmospheric archive of air bubbles enclosed in polar ice cores provides the only direct record of greenhouse gas changes in the past, and the key to understanding the related changes in biogeochemical cycles and climate/greenhouse gas feedbacks.
Crucial questions about greenhouse gas variability on very short (decadal) and very long (orbital) time scales still remain open. To answer these questions, the ice core community has proposed new drilling projects with the goal of nearly doubling the time span of the available ice core record to the last 1.5 million years and of covering the entire Holocene greenhouse gas record in unprecedented decadal resolution. These goals have one thing in common: due to glacier flow most of this record will only be found in a very thin layer in the bottom-most ice of the cores. Completely new analytical approaches are needed to unlock the atmospheric archive in this ice in order to gain high-resolution, high-precision measurements, while at the same time drastically reducing sample consumption compared to established techniques.
The deepSLice project will make such a step change in ice core analytics by developing a novel coupled Continuous Sublimation Extraction-Quantum Cascade Laser Spectrometer system. It will allow us to simultaneously measure CO2, CH4 and N2O concentrations as well as the isotopic composition of CO2 on air samples of only 1-2 ml at standard pressure and temperature, reducing the required sample size by one order of magnitude. This non-destructive analysis will make it also possible for the complete air sample to be recollected after analysis and used for other measurements. This method will be applied to existing and new ice cores in order to study past changes in greenhouse gases and the underlying biogeochemical cycles in unparalleled detail.
Summary
The recent anthropogenic global warming makes a detailed understanding of coupling processes between climate and biogeochemical cycles of pressing importance. The atmospheric archive of air bubbles enclosed in polar ice cores provides the only direct record of greenhouse gas changes in the past, and the key to understanding the related changes in biogeochemical cycles and climate/greenhouse gas feedbacks.
Crucial questions about greenhouse gas variability on very short (decadal) and very long (orbital) time scales still remain open. To answer these questions, the ice core community has proposed new drilling projects with the goal of nearly doubling the time span of the available ice core record to the last 1.5 million years and of covering the entire Holocene greenhouse gas record in unprecedented decadal resolution. These goals have one thing in common: due to glacier flow most of this record will only be found in a very thin layer in the bottom-most ice of the cores. Completely new analytical approaches are needed to unlock the atmospheric archive in this ice in order to gain high-resolution, high-precision measurements, while at the same time drastically reducing sample consumption compared to established techniques.
The deepSLice project will make such a step change in ice core analytics by developing a novel coupled Continuous Sublimation Extraction-Quantum Cascade Laser Spectrometer system. It will allow us to simultaneously measure CO2, CH4 and N2O concentrations as well as the isotopic composition of CO2 on air samples of only 1-2 ml at standard pressure and temperature, reducing the required sample size by one order of magnitude. This non-destructive analysis will make it also possible for the complete air sample to be recollected after analysis and used for other measurements. This method will be applied to existing and new ice cores in order to study past changes in greenhouse gases and the underlying biogeochemical cycles in unparalleled detail.
Max ERC Funding
2 255 788 €
Duration
Start date: 2015-10-01, End date: 2021-03-31
