Project acronym PROTEOMICS V3.0
Project Proteomics v3.0: Development, Implementation and Dissemination of a Third Generation Proteomics Technology
Researcher (PI) Rudolf Aebersold
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Quantitative proteomics is a key technology for the life sciences in general and for systems biology in particular. So far, however, technical limitations have made it impossible to analyze the complete proteome of any species. It is the general goal of this proposal to develop, implement, apply and disseminate a new proteomic strategy that has the potential to generate quantitative proteomic datasets at an unprecedented depth, throughput, accuracy and robustness. Specifically, the new technology will identify and quantify every protein in a proteome. The title of the project Proteomics v3.0 was chosen to indicate the transformation of proteomics into its third phase, after 2D gel electrophoresis and LC-MS/MS based shotgun proteomics. Proteomics v3.0 is based on two sequential steps, emulating the strategy that has been immensely successful in the genomic sciences. In the first step the proteomic space is completely mapped out to generate a proteomic resource that is akin to the genomic sequence database. In the second step rapid and accurate assays will be developed to unambiguously identify and quantify any protein of the respective proteome in a multitude of samples. These assays will be made publicly accessible to support quantitative proteomic studies in the respective species. The strategy will first be implemented and tested in the yeast S. cerevisiae. In a later stage of the project it will be extended to the more complicated human proteome and include the development of assays that also probe the state of modification, splice forms and other types of protein variants generated by a specific open reading frame. Overall, the project will transform quantitative proteomics from a highly specialized technology practiced at a high level in a few laboratories worldwide into a commodity technology accessible, in principle to every group.
Summary
Quantitative proteomics is a key technology for the life sciences in general and for systems biology in particular. So far, however, technical limitations have made it impossible to analyze the complete proteome of any species. It is the general goal of this proposal to develop, implement, apply and disseminate a new proteomic strategy that has the potential to generate quantitative proteomic datasets at an unprecedented depth, throughput, accuracy and robustness. Specifically, the new technology will identify and quantify every protein in a proteome. The title of the project Proteomics v3.0 was chosen to indicate the transformation of proteomics into its third phase, after 2D gel electrophoresis and LC-MS/MS based shotgun proteomics. Proteomics v3.0 is based on two sequential steps, emulating the strategy that has been immensely successful in the genomic sciences. In the first step the proteomic space is completely mapped out to generate a proteomic resource that is akin to the genomic sequence database. In the second step rapid and accurate assays will be developed to unambiguously identify and quantify any protein of the respective proteome in a multitude of samples. These assays will be made publicly accessible to support quantitative proteomic studies in the respective species. The strategy will first be implemented and tested in the yeast S. cerevisiae. In a later stage of the project it will be extended to the more complicated human proteome and include the development of assays that also probe the state of modification, splice forms and other types of protein variants generated by a specific open reading frame. Overall, the project will transform quantitative proteomics from a highly specialized technology practiced at a high level in a few laboratories worldwide into a commodity technology accessible, in principle to every group.
Max ERC Funding
2 400 000 €
Duration
Start date: 2009-04-01, End date: 2014-03-31
Project acronym REGULATORYCIRCUITS
Project Novel Systematic Strategies for Elucidating Cellular Regulatory Circuits
Researcher (PI) Nir Friedman
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary The precise regulation of gene expression has been the subject of extensive scrutiny. Nonetheless, there is a big gap between genomic characterization of transcriptional responses and our predictions based on known molecular mechanisms and networks and of transcription regulation. In this proposal I argue for an approach to bridge this gap by using a novel experimental strategy that exploits the recent maturation of two technologies: the use of fluorescence reporter techniques to monitor promoter activity and high-throughput genetic manipulations for the construction of combinatorial genetic perturbations. By combining these, we will screen for genes that modulate the transcriptional response of target promoters, use genetic interactions between them to better resolve their functional dependencies, and build detailed quantitative models of transcriptional processes. We will use the budding yeast model organism, which allows for efficient manipulations, to dissect two transcriptional responses that are prototypical of many regulatory networks in living cells: [1] The early response to osmotic stress, which is mediated by at least two signaling pathways and multiple transcription factors, and [2] the central carbon metabolism response to shifts in carbon source, which involves multiple sensing and signaling pathways to maintain homeostasis. Our approach will elucidate mechanisms that are opaque to classical screens and facilitate building detailed predictive models of these responses. These results will lead to understanding of general principles that govern transcriptional networks. This is the first approach to comprehensively characterize the molecular mechanisms that modulate a transcriptional response, and arrange them in a coherent network. It will open many questions for detailed biochemical investigations, as well as set the stage to extend these ideas to use more detailed phenotypic assays and in more complex organisms.
Summary
The precise regulation of gene expression has been the subject of extensive scrutiny. Nonetheless, there is a big gap between genomic characterization of transcriptional responses and our predictions based on known molecular mechanisms and networks and of transcription regulation. In this proposal I argue for an approach to bridge this gap by using a novel experimental strategy that exploits the recent maturation of two technologies: the use of fluorescence reporter techniques to monitor promoter activity and high-throughput genetic manipulations for the construction of combinatorial genetic perturbations. By combining these, we will screen for genes that modulate the transcriptional response of target promoters, use genetic interactions between them to better resolve their functional dependencies, and build detailed quantitative models of transcriptional processes. We will use the budding yeast model organism, which allows for efficient manipulations, to dissect two transcriptional responses that are prototypical of many regulatory networks in living cells: [1] The early response to osmotic stress, which is mediated by at least two signaling pathways and multiple transcription factors, and [2] the central carbon metabolism response to shifts in carbon source, which involves multiple sensing and signaling pathways to maintain homeostasis. Our approach will elucidate mechanisms that are opaque to classical screens and facilitate building detailed predictive models of these responses. These results will lead to understanding of general principles that govern transcriptional networks. This is the first approach to comprehensively characterize the molecular mechanisms that modulate a transcriptional response, and arrange them in a coherent network. It will open many questions for detailed biochemical investigations, as well as set the stage to extend these ideas to use more detailed phenotypic assays and in more complex organisms.
Max ERC Funding
2 199 899 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym VARB
Project Variability and Robustness in Bio-molecular systems
Researcher (PI) Naama Barkai
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Cells process information using biochemical networks of interacting proteins and genes. We wish to understand the principles that guide the design of such networks. In particular, we are interested in the interplay between variability, inherent to biological systems, and the precision of cellular computing. To better understand this interplay, we will: (1) Characterize the extent of gene expression variability and define its genetic determinants, (2) Reveal how variability is buffered and (3) Describe instances where variability (or 'noise') is an integral part of cellular computation. The study will be conducted in the multidisciplinary atmosphere of our lab, by students trained in physics, computer science, chemistry and biology. Specific issues include: 1. Gene expression variability: we will focus on the influence of chromatin structure on gene expression variability, as suggested by our bioinformatics analysis. 2. Robustness and scaling in embryonic patterning: We will study the means by which fluctuations are buffered during the development of multicellular organisms. We will focus on the robustness of morphogen gradients to protein levels, and on the ability to maintain proportionate pattern in tissues of different size. 3. Noise-driven transitions in a fluctuating environment: Our preliminary results suggest that noise plays an integral part in phosphate homeostasis in S. cerevisiae. We will characterize the role of noise in this system and study its evolutionary implications. Together, our study will shed light on one we believe to be the fundamental challenge of biological information processing: ensuring a reliable and reproducible function in the highly variable biological environment. Our study will furthermore define novel multidisciplinary, system-level paradigms and approaches that will guide further studies of bio-molecular systems
Summary
Cells process information using biochemical networks of interacting proteins and genes. We wish to understand the principles that guide the design of such networks. In particular, we are interested in the interplay between variability, inherent to biological systems, and the precision of cellular computing. To better understand this interplay, we will: (1) Characterize the extent of gene expression variability and define its genetic determinants, (2) Reveal how variability is buffered and (3) Describe instances where variability (or 'noise') is an integral part of cellular computation. The study will be conducted in the multidisciplinary atmosphere of our lab, by students trained in physics, computer science, chemistry and biology. Specific issues include: 1. Gene expression variability: we will focus on the influence of chromatin structure on gene expression variability, as suggested by our bioinformatics analysis. 2. Robustness and scaling in embryonic patterning: We will study the means by which fluctuations are buffered during the development of multicellular organisms. We will focus on the robustness of morphogen gradients to protein levels, and on the ability to maintain proportionate pattern in tissues of different size. 3. Noise-driven transitions in a fluctuating environment: Our preliminary results suggest that noise plays an integral part in phosphate homeostasis in S. cerevisiae. We will characterize the role of noise in this system and study its evolutionary implications. Together, our study will shed light on one we believe to be the fundamental challenge of biological information processing: ensuring a reliable and reproducible function in the highly variable biological environment. Our study will furthermore define novel multidisciplinary, system-level paradigms and approaches that will guide further studies of bio-molecular systems
Max ERC Funding
2 200 000 €
Duration
Start date: 2009-01-01, End date: 2013-10-31
