Project acronym ABYSS
Project ABYSS - Assessment of bacterial life and matter cycling in deep-sea surface sediments
Researcher (PI) Antje Boetius
Host Institution (HI) ALFRED-WEGENER-INSTITUT HELMHOLTZ-ZENTRUM FUR POLAR- UND MEERESFORSCHUNG
Country Germany
Call Details Advanced Grant (AdG), LS8, ERC-2011-ADG_20110310
Summary The deep-sea floor hosts a distinct microbial biome covering 67% of the Earth’s surface, characterized by cold temperatures, permanent darkness, high pressure and food limitation. The surface sediments are dominated by bacteria, with on average a billion cells per ml. Benthic bacteria are highly relevant to the Earth’s element cycles as they remineralize most of the organic matter sinking from the productive surface ocean, and return nutrients, thereby promoting ocean primary production. What passes the bacterial filter is a relevant sink for carbon on geological time scales, influencing global oxygen and carbon budgets, and fueling the deep subsurface biosphere. Despite the relevance of deep-sea sediment bacteria to climate, geochemical cycles and ecology of the seafloor, their genetic and functional diversity, niche differentiation and biological interactions remain unknown. Our preliminary work in a global survey of deep-sea sediments enables us now to target specific genes for the quantification of abyssal bacteria. We can trace isotope-labeled elements into communities and single cells, and analyze the molecular alteration of organic matter during microbial degradation, all in context with environmental dynamics recorded at the only long-term deep-sea ecosystem observatory in the Arctic that we maintain. I propose to bridge biogeochemistry, ecology, microbiology and marine biology to develop a systematic understanding of abyssal sediment bacterial community distribution, diversity, function and interactions, by combining in situ flux studies and different visualization techniques with a wide range of molecular tools. Substantial progress is expected in understanding I) identity and function of the dominant types of indigenous benthic bacteria, II) dynamics in bacterial activity and diversity caused by variations in particle flux, III) interactions with different types and ages of organic matter, and other biological factors.
Summary
The deep-sea floor hosts a distinct microbial biome covering 67% of the Earth’s surface, characterized by cold temperatures, permanent darkness, high pressure and food limitation. The surface sediments are dominated by bacteria, with on average a billion cells per ml. Benthic bacteria are highly relevant to the Earth’s element cycles as they remineralize most of the organic matter sinking from the productive surface ocean, and return nutrients, thereby promoting ocean primary production. What passes the bacterial filter is a relevant sink for carbon on geological time scales, influencing global oxygen and carbon budgets, and fueling the deep subsurface biosphere. Despite the relevance of deep-sea sediment bacteria to climate, geochemical cycles and ecology of the seafloor, their genetic and functional diversity, niche differentiation and biological interactions remain unknown. Our preliminary work in a global survey of deep-sea sediments enables us now to target specific genes for the quantification of abyssal bacteria. We can trace isotope-labeled elements into communities and single cells, and analyze the molecular alteration of organic matter during microbial degradation, all in context with environmental dynamics recorded at the only long-term deep-sea ecosystem observatory in the Arctic that we maintain. I propose to bridge biogeochemistry, ecology, microbiology and marine biology to develop a systematic understanding of abyssal sediment bacterial community distribution, diversity, function and interactions, by combining in situ flux studies and different visualization techniques with a wide range of molecular tools. Substantial progress is expected in understanding I) identity and function of the dominant types of indigenous benthic bacteria, II) dynamics in bacterial activity and diversity caused by variations in particle flux, III) interactions with different types and ages of organic matter, and other biological factors.
Max ERC Funding
3 375 693 €
Duration
Start date: 2012-06-01, End date: 2018-05-31
Project acronym ACCOMPLI
Project Assembly and maintenance of a co-regulated chromosomal compartment
Researcher (PI) Peter Burkhard Becker
Host Institution (HI) LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Country Germany
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary "Eukaryotic nuclei are organised into functional compartments, – local microenvironments that are enriched in certain molecules or biochemical activities and therefore specify localised functional outputs. Our study seeks to unveil fundamental principles of co-regulation of genes in a chromo¬somal compartment and the preconditions for homeostasis of such a compartment in the dynamic nuclear environment.
The dosage-compensated X chromosome of male Drosophila flies satisfies the criteria for a functional com¬partment. It is rendered structurally distinct from all other chromosomes by association of a regulatory ribonucleoprotein ‘Dosage Compensation Complex’ (DCC), enrichment of histone modifications and global decondensation. As a result, most genes on the X chromosome are co-ordinately activated. Autosomal genes inserted into the X acquire X-chromosomal features and are subject to the X-specific regulation.
We seek to uncover the molecular principles that initiate, establish and maintain the dosage-compensated chromosome. We will follow the kinetics of DCC assembly and the timing of association with different types of chromosomal targets in nuclei with high spatial resolution afforded by sub-wavelength microscopy and deep sequencing of DNA binding sites. We will characterise DCC sub-complexes with respect to their roles as kinetic assembly intermediates or as representations of local, functional heterogeneity. We will evaluate the roles of a DCC- novel ubiquitin ligase activity for homeostasis.
Crucial to the recruitment of the DCC and its distribution to target genes are non-coding roX RNAs that are transcribed from the X. We will determine the secondary structure ‘signatures’ of roX RNAs in vitro and determine the binding sites of the protein subunits in vivo. By biochemical and cellular reconstitution will test the hypothesis that roX-encoded RNA aptamers orchestrate the assembly of the DCC and contribute to the exquisite targeting of the complex."
Summary
"Eukaryotic nuclei are organised into functional compartments, – local microenvironments that are enriched in certain molecules or biochemical activities and therefore specify localised functional outputs. Our study seeks to unveil fundamental principles of co-regulation of genes in a chromo¬somal compartment and the preconditions for homeostasis of such a compartment in the dynamic nuclear environment.
The dosage-compensated X chromosome of male Drosophila flies satisfies the criteria for a functional com¬partment. It is rendered structurally distinct from all other chromosomes by association of a regulatory ribonucleoprotein ‘Dosage Compensation Complex’ (DCC), enrichment of histone modifications and global decondensation. As a result, most genes on the X chromosome are co-ordinately activated. Autosomal genes inserted into the X acquire X-chromosomal features and are subject to the X-specific regulation.
We seek to uncover the molecular principles that initiate, establish and maintain the dosage-compensated chromosome. We will follow the kinetics of DCC assembly and the timing of association with different types of chromosomal targets in nuclei with high spatial resolution afforded by sub-wavelength microscopy and deep sequencing of DNA binding sites. We will characterise DCC sub-complexes with respect to their roles as kinetic assembly intermediates or as representations of local, functional heterogeneity. We will evaluate the roles of a DCC- novel ubiquitin ligase activity for homeostasis.
Crucial to the recruitment of the DCC and its distribution to target genes are non-coding roX RNAs that are transcribed from the X. We will determine the secondary structure ‘signatures’ of roX RNAs in vitro and determine the binding sites of the protein subunits in vivo. By biochemical and cellular reconstitution will test the hypothesis that roX-encoded RNA aptamers orchestrate the assembly of the DCC and contribute to the exquisite targeting of the complex."
Max ERC Funding
2 482 770 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym CARDIOSPLICE
Project A systems and targeted approach to alternative splicing in the developing and diseased heart: Translating basic cell biology to improved cardiac function
Researcher (PI) Michael Gotthardt
Host Institution (HI) MAX DELBRUECK CENTRUM FUER MOLEKULARE MEDIZIN IN DER HELMHOLTZ-GEMEINSCHAFT (MDC)
Country Germany
Call Details Starting Grant (StG), LS4, ERC-2011-StG_20101109
Summary Cardiovascular disease keeps the top spot in mortality statistics in Europe with 2 million deaths annually and although prevention and therapy have continuously been improved, the prevalence of heart failure continues to rise. While contractile (systolic) dysfunction is readily accessible to pharmacological treatment, there is a lack of therapeutic options for reduced ventricular filling (diastolic dysfunction). The diastolic properties of the heart are largely determined by the giant sarcomeric protein titin, which is alternatively spliced to adjust the elastic properties of the cardiomyocyte. We have recently identified a titin splice factor that plays a parallel role in cardiac disease and postnatal development. It targets a subset of genes that concertedly affect biomechanics, electrical activity, and signal transduction and suggests alternative splicing as a novel therapeutic target in heart disease. Here we will build on the titin splice factor to identify regulatory principles and cofactors that adjust cardiac isoform expression. In a complementary approach we will investigate titin mRNA binding proteins to provide a comprehensive analysis of factors governing titin’s differential splicing in cardiac development, health, and disease. Based on its distinctive role in ventricular filling we will evaluate titin splicing as a therapeutic target in diastolic heart failure and use a titin based reporter assay to identify small molecules to interfere with titin isoform expression. Finally, we will evaluate the effects of altered alternative splicing on diastolic dysfunction in vivo utilizing the splice deficient mutant and our available animal models for diastolic dysfunction.
The overall scientific goal of the proposed work is to investigate the regulation of cardiac alternative splicing in development and disease and to evaluate if splice directed therapy can be used to improve diastolic function and specifically the elastic properties of the heart.
Summary
Cardiovascular disease keeps the top spot in mortality statistics in Europe with 2 million deaths annually and although prevention and therapy have continuously been improved, the prevalence of heart failure continues to rise. While contractile (systolic) dysfunction is readily accessible to pharmacological treatment, there is a lack of therapeutic options for reduced ventricular filling (diastolic dysfunction). The diastolic properties of the heart are largely determined by the giant sarcomeric protein titin, which is alternatively spliced to adjust the elastic properties of the cardiomyocyte. We have recently identified a titin splice factor that plays a parallel role in cardiac disease and postnatal development. It targets a subset of genes that concertedly affect biomechanics, electrical activity, and signal transduction and suggests alternative splicing as a novel therapeutic target in heart disease. Here we will build on the titin splice factor to identify regulatory principles and cofactors that adjust cardiac isoform expression. In a complementary approach we will investigate titin mRNA binding proteins to provide a comprehensive analysis of factors governing titin’s differential splicing in cardiac development, health, and disease. Based on its distinctive role in ventricular filling we will evaluate titin splicing as a therapeutic target in diastolic heart failure and use a titin based reporter assay to identify small molecules to interfere with titin isoform expression. Finally, we will evaluate the effects of altered alternative splicing on diastolic dysfunction in vivo utilizing the splice deficient mutant and our available animal models for diastolic dysfunction.
The overall scientific goal of the proposed work is to investigate the regulation of cardiac alternative splicing in development and disease and to evaluate if splice directed therapy can be used to improve diastolic function and specifically the elastic properties of the heart.
Max ERC Funding
1 499 191 €
Duration
Start date: 2012-01-01, End date: 2017-06-30
Project acronym CelluFuel
Project Designer Cellulosomes by Single Molecule Cut & Paste
Researcher (PI) Hermann Eduard Gaub
Host Institution (HI) LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Country Germany
Call Details Advanced Grant (AdG), LS1, ERC-2011-ADG_20110310
Summary Biofuel from wood and waste will be a substantial share of our future energy mix. The conversion of lignocellulose to fermentable polysaccharides is the current bottleneck. We propose to use single molecule cut and paste technology to assemble designer cellulosoms and combine enzymes from different species with nanocatalysts.
Summary
Biofuel from wood and waste will be a substantial share of our future energy mix. The conversion of lignocellulose to fermentable polysaccharides is the current bottleneck. We propose to use single molecule cut and paste technology to assemble designer cellulosoms and combine enzymes from different species with nanocatalysts.
Max ERC Funding
2 351 450 €
Duration
Start date: 2012-03-01, End date: 2018-02-28
Project acronym CHIRALMICROBOTS
Project Chiral Nanostructured Surfaces and Colloidal Microbots
Researcher (PI) Peer Fischer
Host Institution (HI) Klinik Max Planck Institut für Psychiatrie
Country Germany
Call Details Starting Grant (StG), PE4, ERC-2011-StG_20101014
Summary "From scientific publications to the popular media, there have been numerous speculations about wirelessly controlled microrobots (microbots) navigating the human body. Microbots have the potential to revolutionize analytics, targeted drug delivery, and microsurgery, but until now there has not been any untethered microscopic system that could be properly moved let alone controlled in fluidic environments. Using glancing angle (physical vapor deposition) we will grow billions of micron-sized colloidal screw-propellers on a wafer. These chiral mesoscopic screws can be magnetized and moved through solution under computer control. The screw-propellers resemble artificial flagella and are the only ‘microbots’ to date that can be fully controlled in solution at micron length scales. The proposed work will advance the fabrication so that active microbots can be applied in rheological measurements and analytics. We will use these novel probes in bio-microrheology with the potential to probe the viscoelastic properties of membranes and tissues, and to explore questions of micro-hydrodynamics. At the same time we will develop these structures as ""colloidal molecules"" and grow asymmetric mesoscopic particles with tailored shapes and properties. We propose experiments that allow the observation of fundamental effects, such as chiral Brownian motion, something that exist at the molecular scale, but has never been observed to date. Similarly, we will be able to demonstrate for the first time chiral separations based purely on physical fields. The proposed technical advances of the growth of nanostructured surfaces will at the same time permit wafer-scale 3-D nano-structuring for photonic and plasmonic applications, which we plan to demonstrate. We will develop a system for targeted drug delivery, study the interaction of swarms of microbots and devise techniques to control and image these swarms."
Summary
"From scientific publications to the popular media, there have been numerous speculations about wirelessly controlled microrobots (microbots) navigating the human body. Microbots have the potential to revolutionize analytics, targeted drug delivery, and microsurgery, but until now there has not been any untethered microscopic system that could be properly moved let alone controlled in fluidic environments. Using glancing angle (physical vapor deposition) we will grow billions of micron-sized colloidal screw-propellers on a wafer. These chiral mesoscopic screws can be magnetized and moved through solution under computer control. The screw-propellers resemble artificial flagella and are the only ‘microbots’ to date that can be fully controlled in solution at micron length scales. The proposed work will advance the fabrication so that active microbots can be applied in rheological measurements and analytics. We will use these novel probes in bio-microrheology with the potential to probe the viscoelastic properties of membranes and tissues, and to explore questions of micro-hydrodynamics. At the same time we will develop these structures as ""colloidal molecules"" and grow asymmetric mesoscopic particles with tailored shapes and properties. We propose experiments that allow the observation of fundamental effects, such as chiral Brownian motion, something that exist at the molecular scale, but has never been observed to date. Similarly, we will be able to demonstrate for the first time chiral separations based purely on physical fields. The proposed technical advances of the growth of nanostructured surfaces will at the same time permit wafer-scale 3-D nano-structuring for photonic and plasmonic applications, which we plan to demonstrate. We will develop a system for targeted drug delivery, study the interaction of swarms of microbots and devise techniques to control and image these swarms."
Max ERC Funding
1 479 760 €
Duration
Start date: 2012-02-01, End date: 2018-01-31
Project acronym CLOCKWORKGREEN
Project Ecological performance of arrhythmic plants in nature
Researcher (PI) Ian Thomas Baldwin
Host Institution (HI) Klinik Max Planck Institut für Psychiatrie
Country Germany
Call Details Advanced Grant (AdG), LS8, ERC-2011-ADG_20110310
Summary Timing is everything in ecology, and because plants provide the foundation for most land-based food webs, the timing of their activities profoundly orchestrates the majority of ecological interactions. Most photosynthetic and growth processes are under circadian control, but many additional processes--approximately 30-40% of all genes—are under circadian control, and yet the Darwinian fitness impact of being “in synch” with the environment has not been systematically studied for any organism.
We have developed a toolbox for a native tobacco plant, Nicotiana attenuata, that allows us to “ask the plant” which genes, proteins or metabolites are regulated in particular plant-mediated ecological interactions; identify “the genes that matter” for a given interaction; silence or ectopically express these genes, and conduct field releases with the transformed plants at a nature preserve in the Great Basin Desert to rigorously test hypotheses of gene function. By taking advantage of both our understanding of what it takes for this plant to survive in nature, and the procedures established to disentangle the skein of subtle interactions that determine its performance, we will systematically examine the importance of synchronous entrained endogenous rhythms at all life stages: longevity in the seed bank, germination, rosette growth, elongation, flowering and senescence. Specifically, we propose to silence a key components (starting with NaTOC1) of the plant’s endogenous clock to shorten the plant’s circadian rhythm, both constitutively and with strong dexamethasone-inducible promoters, at all life stages. With a combination of real-time phenotype imaging, metabolite and transcriptome analysis, and ecological know-how, the research will reveal how plants adjust their physiologies to the ever-changing panoply of environmental stresses with which they must cope; by creating arrhythmic plants, we will understand why so many processes are under circadian control.
Summary
Timing is everything in ecology, and because plants provide the foundation for most land-based food webs, the timing of their activities profoundly orchestrates the majority of ecological interactions. Most photosynthetic and growth processes are under circadian control, but many additional processes--approximately 30-40% of all genes—are under circadian control, and yet the Darwinian fitness impact of being “in synch” with the environment has not been systematically studied for any organism.
We have developed a toolbox for a native tobacco plant, Nicotiana attenuata, that allows us to “ask the plant” which genes, proteins or metabolites are regulated in particular plant-mediated ecological interactions; identify “the genes that matter” for a given interaction; silence or ectopically express these genes, and conduct field releases with the transformed plants at a nature preserve in the Great Basin Desert to rigorously test hypotheses of gene function. By taking advantage of both our understanding of what it takes for this plant to survive in nature, and the procedures established to disentangle the skein of subtle interactions that determine its performance, we will systematically examine the importance of synchronous entrained endogenous rhythms at all life stages: longevity in the seed bank, germination, rosette growth, elongation, flowering and senescence. Specifically, we propose to silence a key components (starting with NaTOC1) of the plant’s endogenous clock to shorten the plant’s circadian rhythm, both constitutively and with strong dexamethasone-inducible promoters, at all life stages. With a combination of real-time phenotype imaging, metabolite and transcriptome analysis, and ecological know-how, the research will reveal how plants adjust their physiologies to the ever-changing panoply of environmental stresses with which they must cope; by creating arrhythmic plants, we will understand why so many processes are under circadian control.
Max ERC Funding
2 496 002 €
Duration
Start date: 2012-04-01, End date: 2017-03-31
Project acronym COMBIPATTERNING
Project Combinatorial Patterning of Particles for High Density Peptide Arrays
Researcher (PI) Alexander Nesterov-Mueller
Host Institution (HI) KARLSRUHER INSTITUT FUER TECHNOLOGIE
Country Germany
Call Details Starting Grant (StG), PE8, ERC-2011-StG_20101014
Summary We want to use selective laser melting to pattern a substrate with different solid micro particles at a density of 1 million spots per cm2. First, a homogeneous particle layer is deposited on a substrate and a pattern of micro spots of melted matrix is generated by laser radiation. Then, non-melted particles are blown away. Embedded within the particles are different chemically reactive amino acid derivatives that will start coupling to very small synthesis sites upon melting the particle pattern in an oven. This is done once all of the 20 different amino acid particles have been glued by laser patterning to the surface. Washing away uncoupled material, removing Fmoc protecting group, and repeating the patterning steps according to standard Merrifield synthesis, leads to the combinatorial synthesis of very high-density peptide arrays. The main objective of this proposal is to develop this method up to the level of a semi-automated synthesis machine. In addition, we will use the manufactured very high-density peptide arrays to readout the information that is deposited in the immune system, i.e. find a peptide binder for every one of the 200-500 antibody species that patrol the serum of an individual in elevated levels. These experiments might lead to novel tools to find out the causes of hitherto enigmatic diseases because then we might be able to correlate antibody patterns with disease status without knowing in advance the disease-specific antibodies. Beyond the life sciences, we want to embed 10.000 peptides per cm2 within an insulating layer of alkane thiols, each on a different gold pad of a specially designed screening chip. Then, we could readout I/V characteristics of individual peptide species, and eventually find peptide-based diodes. These could be modified in their sequence and screened again for better performance. This evolution-inspired screening approach might lead to novel materials that could be used in fuel cells.
Summary
We want to use selective laser melting to pattern a substrate with different solid micro particles at a density of 1 million spots per cm2. First, a homogeneous particle layer is deposited on a substrate and a pattern of micro spots of melted matrix is generated by laser radiation. Then, non-melted particles are blown away. Embedded within the particles are different chemically reactive amino acid derivatives that will start coupling to very small synthesis sites upon melting the particle pattern in an oven. This is done once all of the 20 different amino acid particles have been glued by laser patterning to the surface. Washing away uncoupled material, removing Fmoc protecting group, and repeating the patterning steps according to standard Merrifield synthesis, leads to the combinatorial synthesis of very high-density peptide arrays. The main objective of this proposal is to develop this method up to the level of a semi-automated synthesis machine. In addition, we will use the manufactured very high-density peptide arrays to readout the information that is deposited in the immune system, i.e. find a peptide binder for every one of the 200-500 antibody species that patrol the serum of an individual in elevated levels. These experiments might lead to novel tools to find out the causes of hitherto enigmatic diseases because then we might be able to correlate antibody patterns with disease status without knowing in advance the disease-specific antibodies. Beyond the life sciences, we want to embed 10.000 peptides per cm2 within an insulating layer of alkane thiols, each on a different gold pad of a specially designed screening chip. Then, we could readout I/V characteristics of individual peptide species, and eventually find peptide-based diodes. These could be modified in their sequence and screened again for better performance. This evolution-inspired screening approach might lead to novel materials that could be used in fuel cells.
Max ERC Funding
1 494 600 €
Duration
Start date: 2011-11-01, End date: 2016-10-31
Project acronym COMPLEX_TRAITS
Project High-throughput dissection of the genetics underlying complex traits
Researcher (PI) Lars Steinmetz
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Country Germany
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary The vast majority of genetic diseases are complex traits, conditioned by multiple genetic and environmental factors. Yet our understanding of the genetics underlying such traits in humans remains extremely limited, due largely to the statistical complexity of inferring the effects of allelic variants in a genetically diverse population. Novel tools for the dissection of the genetic architecture of complex traits, therefore, can be most effectively developed in model organisms, where the contribution of individual alleles can be quantitatively determined in controlled genetic backgrounds. We have previously established the yeast Saccharomyces cerevisiae as a model for complex traits by unravelling complex genetic architectures that govern quantitative phenotypes in this organism. We achieved this by pioneering approaches that have revealed crucial information about the complexity of the underlying genetics. Here we propose to advance to the next level of complex trait dissection by developing systematic, genome-wide technologies that aim to identify all of the variants underlying a complex trait in a single step. In particular, we will investigate traits involved in mitochondrial function, which are both clinically relevant and highly conserved in yeast. Our combination of genomic technologies will allow us to: 1) systematically detect, with maximal sensitivity, the majority of genetic variants (coding and non-coding) that condition these traits; 2) quantify the contributions of these variants and their interactions; and 3) evaluate the strengths and limitations of current methods for dissecting complex traits. Taken together, our research will yield fundamental insights into the genetic complexity of multifactorial traits, providing valuable lessons and establishing novel genomic tools that will facilitate the investigation of complex diseases.
Summary
The vast majority of genetic diseases are complex traits, conditioned by multiple genetic and environmental factors. Yet our understanding of the genetics underlying such traits in humans remains extremely limited, due largely to the statistical complexity of inferring the effects of allelic variants in a genetically diverse population. Novel tools for the dissection of the genetic architecture of complex traits, therefore, can be most effectively developed in model organisms, where the contribution of individual alleles can be quantitatively determined in controlled genetic backgrounds. We have previously established the yeast Saccharomyces cerevisiae as a model for complex traits by unravelling complex genetic architectures that govern quantitative phenotypes in this organism. We achieved this by pioneering approaches that have revealed crucial information about the complexity of the underlying genetics. Here we propose to advance to the next level of complex trait dissection by developing systematic, genome-wide technologies that aim to identify all of the variants underlying a complex trait in a single step. In particular, we will investigate traits involved in mitochondrial function, which are both clinically relevant and highly conserved in yeast. Our combination of genomic technologies will allow us to: 1) systematically detect, with maximal sensitivity, the majority of genetic variants (coding and non-coding) that condition these traits; 2) quantify the contributions of these variants and their interactions; and 3) evaluate the strengths and limitations of current methods for dissecting complex traits. Taken together, our research will yield fundamental insights into the genetic complexity of multifactorial traits, providing valuable lessons and establishing novel genomic tools that will facilitate the investigation of complex diseases.
Max ERC Funding
2 499 821 €
Duration
Start date: 2012-11-01, End date: 2017-10-31
Project acronym COMPLEXNMD
Project NMD Complexes: Eukaryotic mRNA Quality Control
Researcher (PI) Christiane Helene Berger-Schaffitzel
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Country Germany
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary Nonsense-mediated mRNA decay (NMD) is an essential mechanism controlling translation in the eukaryotic cell. NMD ascertains accurate expression of the genetic information by quality controlling messenger RNA (mRNA). During translation, NMD factors recognize and target to degradation aberrant mRNAs that have a premature stop codon (PTC) and that would otherwise lead to the production of truncated proteins which could be harmful for the cell. A wide range of genetic diseases have their origin in the mechanisms of NMD. Discrimination of a PTC from a correct termination codon depends on splicing and translation, and it is the first and foremost step in human NMD. The molecular mechanism of this process remains elusive to date.
In the research proposed, I will undertake to elucidate the molecular basis of translation termination and induction of NMD. I will study complexes involved in human translation termination at a normal stop codon and involved in NMD. I will employ an array of innovative techniques including recombinant production of human protein complexes by the MultiBac system, mammalian in vitro translation, mass spectrometry for detecting relevant protein modifications, biophysical techniques, mutational analyses and RNA-interference experiments. Stable ribosomal complexes with termination factors and complexes of NMD factors will be used for structure determination by cryo-electron microscopy. State-of-the-art image processing will be applied to address the inherent heterogeneity of the complexes. Hybrid approaches will allow the combination of cryo-EM structures with existing high-resolution structures of factors involved for generation of quasi-atomic models thereby visualizing molecular mechanisms of NMD action. This interdisciplinary work will foster our understanding at a molecular level of a paramount step in mRNA quality control, which is a vital prerequisite for the development of new treatment strategies in NMD-related diseases.
Summary
Nonsense-mediated mRNA decay (NMD) is an essential mechanism controlling translation in the eukaryotic cell. NMD ascertains accurate expression of the genetic information by quality controlling messenger RNA (mRNA). During translation, NMD factors recognize and target to degradation aberrant mRNAs that have a premature stop codon (PTC) and that would otherwise lead to the production of truncated proteins which could be harmful for the cell. A wide range of genetic diseases have their origin in the mechanisms of NMD. Discrimination of a PTC from a correct termination codon depends on splicing and translation, and it is the first and foremost step in human NMD. The molecular mechanism of this process remains elusive to date.
In the research proposed, I will undertake to elucidate the molecular basis of translation termination and induction of NMD. I will study complexes involved in human translation termination at a normal stop codon and involved in NMD. I will employ an array of innovative techniques including recombinant production of human protein complexes by the MultiBac system, mammalian in vitro translation, mass spectrometry for detecting relevant protein modifications, biophysical techniques, mutational analyses and RNA-interference experiments. Stable ribosomal complexes with termination factors and complexes of NMD factors will be used for structure determination by cryo-electron microscopy. State-of-the-art image processing will be applied to address the inherent heterogeneity of the complexes. Hybrid approaches will allow the combination of cryo-EM structures with existing high-resolution structures of factors involved for generation of quasi-atomic models thereby visualizing molecular mechanisms of NMD action. This interdisciplinary work will foster our understanding at a molecular level of a paramount step in mRNA quality control, which is a vital prerequisite for the development of new treatment strategies in NMD-related diseases.
Max ERC Funding
1 176 825 €
Duration
Start date: 2012-02-01, End date: 2016-11-30
Project acronym COMPNET
Project Dynamics and Self-organisation in Complex Cytoskeletal Networks
Researcher (PI) Andreas Bausch
Host Institution (HI) TECHNISCHE UNIVERSITAET MUENCHEN
Country Germany
Call Details Starting Grant (StG), PE3, ERC-2011-StG_20101014
Summary The requirements on the eukaryotic cytoskeleton are not only of high complexity, but include demands that are actually contradictory in the first place: While the dynamic character of cytoskeletal structures is essential for the motility of cells, their ability for morphological reorganisations and cell division, the structural integrity of cells relies on the stability of cytoskeletal structures. From a biophysical point of view, this dynamic structure formation and stabilization stems from a self-organisation process that is tightly controlled by the simultaneous and competing function of a plethora of actin binding proteins (ABPs). To understand the self-organisation phenomena observed in the cytoskeleton it is therefore indispensable to first shed light on the functional role of ABPs and their underlying molecular mechanisms. Hereby development of reliable reconstituted model systems as has been proven by the great progress achieved in our understanding of individual crosslinking proteins that turn the cytoskeleton into a viscoelastic physical gel. The advantage of such reconstituted systems is that the biological complexity is decreased to an accessible level that the physical principles can be explored and identified.
It is the aim of the present proposal to successively increase the complexity in a well defined manner to further progress in understanding the functional units of a cell. On the way to a sound physical understanding of cellular self organizing principles, the planned major step comprises the incorporation of active processes like the active (de-)polymerisation of filaments and motor mediated active reorganisation and contraction. We plan to develop new tools and approaches to address how the different kinds of ABPs are interacting with each other and how the structure, dynamics and function of the cytoskeleton is locally governed by the competition and interplay between them.
Summary
The requirements on the eukaryotic cytoskeleton are not only of high complexity, but include demands that are actually contradictory in the first place: While the dynamic character of cytoskeletal structures is essential for the motility of cells, their ability for morphological reorganisations and cell division, the structural integrity of cells relies on the stability of cytoskeletal structures. From a biophysical point of view, this dynamic structure formation and stabilization stems from a self-organisation process that is tightly controlled by the simultaneous and competing function of a plethora of actin binding proteins (ABPs). To understand the self-organisation phenomena observed in the cytoskeleton it is therefore indispensable to first shed light on the functional role of ABPs and their underlying molecular mechanisms. Hereby development of reliable reconstituted model systems as has been proven by the great progress achieved in our understanding of individual crosslinking proteins that turn the cytoskeleton into a viscoelastic physical gel. The advantage of such reconstituted systems is that the biological complexity is decreased to an accessible level that the physical principles can be explored and identified.
It is the aim of the present proposal to successively increase the complexity in a well defined manner to further progress in understanding the functional units of a cell. On the way to a sound physical understanding of cellular self organizing principles, the planned major step comprises the incorporation of active processes like the active (de-)polymerisation of filaments and motor mediated active reorganisation and contraction. We plan to develop new tools and approaches to address how the different kinds of ABPs are interacting with each other and how the structure, dynamics and function of the cytoskeleton is locally governed by the competition and interplay between them.
Max ERC Funding
1 495 196 €
Duration
Start date: 2011-10-01, End date: 2012-03-31
