Project acronym BOTTOM-UP_SYSCHEM
Project Systems Chemistry from Bottom Up: Switching, Gating and Oscillations in Non Enzymatic Peptide Networks
Researcher (PI) Gonen Ashkenasy
Host Institution (HI) BEN-GURION UNIVERSITY OF THE NEGEV
Call Details Starting Grant (StG), PE5, ERC-2010-StG_20091028
Summary The study of synthetic molecular networks is of fundamental importance for understanding the organizational principles of biological systems and may well be the key to unraveling the origins of life. In addition, such systems may be useful for parallel synthesis of molecules, implementation of catalysis via multi-step pathways, and as media for various applications in nano-medicine and nano-electronics. We have been involved recently in developing peptide-based replicating networks and revealed their dynamic characteristics. We argue here that the structural information embedded in the polypeptide chains is sufficiently rich to allow the construction of peptide 'Systems Chemistry', namely, to facilitate the use of replicating networks as cell-mimetics, featuring complex dynamic behavior. To bring this novel idea to reality, we plan to take a unique holistic approach by studying such networks both experimentally and via simulations, for elucidating basic-principles and towards applications in adjacent fields, such as molecular electronics. Towards realizing these aims, we will study three separate but inter-related objectives: (i) design and characterization of networks that react and rewire in response to external triggers, such as light, (ii) design of networks that operate via new dynamic rules of product formation that lead to oscillations, and (iii) exploitation of the molecular information gathered from the networks as means to control switching and gating in molecular electronic devices. We believe that achieving the project's objectives will be highly significant for the development of the arising field of Systems Chemistry, and in addition will provide valuable tools for studying related scientific fields, such as systems biology and molecular electronics.
Summary
The study of synthetic molecular networks is of fundamental importance for understanding the organizational principles of biological systems and may well be the key to unraveling the origins of life. In addition, such systems may be useful for parallel synthesis of molecules, implementation of catalysis via multi-step pathways, and as media for various applications in nano-medicine and nano-electronics. We have been involved recently in developing peptide-based replicating networks and revealed their dynamic characteristics. We argue here that the structural information embedded in the polypeptide chains is sufficiently rich to allow the construction of peptide 'Systems Chemistry', namely, to facilitate the use of replicating networks as cell-mimetics, featuring complex dynamic behavior. To bring this novel idea to reality, we plan to take a unique holistic approach by studying such networks both experimentally and via simulations, for elucidating basic-principles and towards applications in adjacent fields, such as molecular electronics. Towards realizing these aims, we will study three separate but inter-related objectives: (i) design and characterization of networks that react and rewire in response to external triggers, such as light, (ii) design of networks that operate via new dynamic rules of product formation that lead to oscillations, and (iii) exploitation of the molecular information gathered from the networks as means to control switching and gating in molecular electronic devices. We believe that achieving the project's objectives will be highly significant for the development of the arising field of Systems Chemistry, and in addition will provide valuable tools for studying related scientific fields, such as systems biology and molecular electronics.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-10-01, End date: 2015-09-30
Project acronym CancerFluxome
Project Cancer Cellular Metabolism across Space and Time
Researcher (PI) Tomer Shlomi
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Call Details Starting Grant (StG), LS2, ERC-2016-STG
Summary The metabolism of cancer cells is altered to meet cellular requirements for growth, providing novel means to selectively target tumorigenesis. While extensively studied, our current view of cancer cellular metabolism is fundamentally limited by lack of information on variability in metabolic activity between distinct subcellular compartments and cells.
We propose to develop a spatio-temporal fluxomics approach for quantifying metabolic fluxes in the cytoplasm vs. mitochondria as well as their cell-cycle dynamics, combining mass-spectrometry based isotope tracing with cell synchronization, rapid cellular fractionation, and computational metabolic network modelling.
Spatio-temporal fluxomics will be used to revisit and challenge our current understanding of central metabolism and its induced adaptation to oncogenic events – an important endeavour considering that mitochondrial bioenergetics and biosynthesis are required for tumorigenesis and accumulating evidences for metabolic alterations throughout the cell-cycle.
Our preliminary results show intriguing oscillations between oxidative and reductive TCA cycle flux throughout the cell-cycle. We will explore the extent to which cells adapt their metabolism to fulfil the changing energetic and anabolic demands throughout the cell-cycle, how metabolic oscillations are regulated, and their benefit to cells in terms of thermodynamic efficiency. Spatial flux analysis will be instrumental for investigating glutaminolysis - a ‘hallmark’ metabolic adaptation in cancer involving shuttling of metabolic intermediates and cofactors between mitochondria and cytoplasm.
On a clinical front, our spatio-temporal fluxomics analysis will enable to disentangle oncogene-induced flux alterations, having an important tumorigenic role, from artefacts originating from population averaging. A comprehensive view of how cells adapt their metabolism due to oncogenic mutations will reveal novel targets for anti-cancer drugs.
Summary
The metabolism of cancer cells is altered to meet cellular requirements for growth, providing novel means to selectively target tumorigenesis. While extensively studied, our current view of cancer cellular metabolism is fundamentally limited by lack of information on variability in metabolic activity between distinct subcellular compartments and cells.
We propose to develop a spatio-temporal fluxomics approach for quantifying metabolic fluxes in the cytoplasm vs. mitochondria as well as their cell-cycle dynamics, combining mass-spectrometry based isotope tracing with cell synchronization, rapid cellular fractionation, and computational metabolic network modelling.
Spatio-temporal fluxomics will be used to revisit and challenge our current understanding of central metabolism and its induced adaptation to oncogenic events – an important endeavour considering that mitochondrial bioenergetics and biosynthesis are required for tumorigenesis and accumulating evidences for metabolic alterations throughout the cell-cycle.
Our preliminary results show intriguing oscillations between oxidative and reductive TCA cycle flux throughout the cell-cycle. We will explore the extent to which cells adapt their metabolism to fulfil the changing energetic and anabolic demands throughout the cell-cycle, how metabolic oscillations are regulated, and their benefit to cells in terms of thermodynamic efficiency. Spatial flux analysis will be instrumental for investigating glutaminolysis - a ‘hallmark’ metabolic adaptation in cancer involving shuttling of metabolic intermediates and cofactors between mitochondria and cytoplasm.
On a clinical front, our spatio-temporal fluxomics analysis will enable to disentangle oncogene-induced flux alterations, having an important tumorigenic role, from artefacts originating from population averaging. A comprehensive view of how cells adapt their metabolism due to oncogenic mutations will reveal novel targets for anti-cancer drugs.
Max ERC Funding
1 481 250 €
Duration
Start date: 2017-02-01, End date: 2022-01-31
Project acronym CrackEpitranscriptom
Project Cracking the epitranscriptome
Researcher (PI) Schraga SCHWARTZ
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2016-STG
Summary Over 100 types of distinct modifications are catalyzed on RNA molecules post-transcriptionally. In an analogous manner to well-studied chemical modifications on proteins or DNA, modifications on RNA - and particularly on mRNA - harbor the exciting potential of regulating the complex and interlinked life cycle of these molecules. The most abundant modification in mammalian and yeast mRNA is N6-methyladenosine (m6A). We have pioneered approaches for mapping m6A in a transcriptome wide manner, and we and others have identified factors involved in encoding and decoding m6A. While experimental disruption of these factors is associated with severe phenotypes, the role of m6A remains enigmatic. No single methylated site has been shown to causally underlie any physiological or molecular function. This proposal aims to establish a framework for systematically deciphering the molecular function of a modification and its underlying mechanisms and to uncover the physiological role of the modification in regulation of a cellular response. We will apply this framework to m6A in the context of meiosis in budding yeast, as m6A dynamically accumulates on meiotic mRNAs and as the methyltransferase catalyzing m6A is essential for meiosis. We will (1) aim to elucidate the physiological targets of methylation governing entry into meiosis (2) seek to elucidate the function of m6A at the molecular level, and understand its impact on the various steps of the mRNA life cycle, (3) seek to understand the mechanisms underlying its effects. These aims will provide a comprehensive framework for understanding how the epitranscriptome, an emerging post-transcriptional layer of regulation, fine-tunes gene regulation and impacts cellular decision making in a dynamic response, and will set the stage towards dissecting the roles of m6A and of an expanding set of mRNA modifications in more complex and disease related systems.
Summary
Over 100 types of distinct modifications are catalyzed on RNA molecules post-transcriptionally. In an analogous manner to well-studied chemical modifications on proteins or DNA, modifications on RNA - and particularly on mRNA - harbor the exciting potential of regulating the complex and interlinked life cycle of these molecules. The most abundant modification in mammalian and yeast mRNA is N6-methyladenosine (m6A). We have pioneered approaches for mapping m6A in a transcriptome wide manner, and we and others have identified factors involved in encoding and decoding m6A. While experimental disruption of these factors is associated with severe phenotypes, the role of m6A remains enigmatic. No single methylated site has been shown to causally underlie any physiological or molecular function. This proposal aims to establish a framework for systematically deciphering the molecular function of a modification and its underlying mechanisms and to uncover the physiological role of the modification in regulation of a cellular response. We will apply this framework to m6A in the context of meiosis in budding yeast, as m6A dynamically accumulates on meiotic mRNAs and as the methyltransferase catalyzing m6A is essential for meiosis. We will (1) aim to elucidate the physiological targets of methylation governing entry into meiosis (2) seek to elucidate the function of m6A at the molecular level, and understand its impact on the various steps of the mRNA life cycle, (3) seek to understand the mechanisms underlying its effects. These aims will provide a comprehensive framework for understanding how the epitranscriptome, an emerging post-transcriptional layer of regulation, fine-tunes gene regulation and impacts cellular decision making in a dynamic response, and will set the stage towards dissecting the roles of m6A and of an expanding set of mRNA modifications in more complex and disease related systems.
Max ERC Funding
1 402 666 €
Duration
Start date: 2016-11-01, End date: 2021-10-31
Project acronym OPTIMLIGHTHARVEST
Project Large Scale Architectures with Nanometric Structured Interfaces for Charge Separation, Transport and Interception
Researcher (PI) Roie Yerushalmi
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Starting Grant (StG), PE5, ERC-2010-StG_20091028
Summary This research is aimed at developing new architectures at the molecular, nanometric, and macroscopic scales for the design and study of light induced charge transport using synthetic systems. The strategic objective is to establish a comprehensive approach for constructing nanometric scale hybrid structures that will enable us to tune the required physical, chemical, and electrical properties across scales required for efficient harvesting of light energy in a rigorous manner for enhancing our capabilities and basic understanding of light harvesting processes. We will form nanometric architectures featuring molecular diversity and functionality with nanometric gaps coupled to scaffolds capable of electrical transport. The nanometric architectures will be formed via simple yet powerful methods relying on sophisticated use of nanostructure surface chemistry and material properties while minimizing the application of top-down fabrication methods and will be studied at the single building block level as well as at array level. Meticulous study of the light induced charge separation and transport at the nanometric scale using single nanostructure building blocks as well as the collective dynamics of large scale arrays will be addressed with an emphasis on understanding charge dynamics at interfaces. The research activity will utilize unique nanostructure assembly methods and post-growth manipulation of the chemical composition developed during my research.
Achieving our fundamental goals is expected to lead to new insights and capabilities relating to the harvesting of light energy and converting it to electrical energy and to significantly advance our ability to utilize light energy for photocatalysis.
Summary
This research is aimed at developing new architectures at the molecular, nanometric, and macroscopic scales for the design and study of light induced charge transport using synthetic systems. The strategic objective is to establish a comprehensive approach for constructing nanometric scale hybrid structures that will enable us to tune the required physical, chemical, and electrical properties across scales required for efficient harvesting of light energy in a rigorous manner for enhancing our capabilities and basic understanding of light harvesting processes. We will form nanometric architectures featuring molecular diversity and functionality with nanometric gaps coupled to scaffolds capable of electrical transport. The nanometric architectures will be formed via simple yet powerful methods relying on sophisticated use of nanostructure surface chemistry and material properties while minimizing the application of top-down fabrication methods and will be studied at the single building block level as well as at array level. Meticulous study of the light induced charge separation and transport at the nanometric scale using single nanostructure building blocks as well as the collective dynamics of large scale arrays will be addressed with an emphasis on understanding charge dynamics at interfaces. The research activity will utilize unique nanostructure assembly methods and post-growth manipulation of the chemical composition developed during my research.
Achieving our fundamental goals is expected to lead to new insights and capabilities relating to the harvesting of light energy and converting it to electrical energy and to significantly advance our ability to utilize light energy for photocatalysis.
Max ERC Funding
1 427 000 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym PROKRNA
Project Prokaryotic RNomics: Unravelling the RNA-mediated regulatory layers
Researcher (PI) Rotem Sorek
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Pioneering studies from the recent year, including those published by the PI of this proposal, are revolutionizing our perception of prokaryotic transcriptomes, and reveal unexpected regulatory complexity. Two central concepts are arising: the unanticipated abundance of cis-antisense RNAs overlapping protein coding genes, and alternative transcripts resulting from a dynamic behaviour of operon structures (where genes can be included or excluded from a polycistronic transcript in response to environmental cues). Understanding these phenomena holds a great potential for our ability to decipher how bacteria regulate their complex life styles and pathogenic behaviours, but their dynamics, regulatory roles, and effects on combinatorially increasing the regulatory capacity of the genome are completely unknown.
The primary objectives of this proposed research are: i) to understand the extent, regulatory roles, and evolutionary consequences of cis-antisense
RNAs in prokaryotes; ii) to understand the regulatory code, combinatorial effects and dynamics of alternative operon structures; and, in parallel iii) to develop a unified framework for comparative prokaryotic transcriptomics.
Our strategy is based on a combination of deep sequencing technologies, computational modelling and data analyses, systems biology
approaches, and focused molecular biology experiments. We will identify the extent and the impact of these RNA-based regulatory layers in representative pathogenic and non-pathogenic species across the prokaryotic tree of life, study their functional and evolutionary consequences, and break the regulatory code controlling them. Our planned research has the potential of producing
methodological and conceptual breakthroughs in the emerging field of prokaryotic transcriptomics.
Summary
Pioneering studies from the recent year, including those published by the PI of this proposal, are revolutionizing our perception of prokaryotic transcriptomes, and reveal unexpected regulatory complexity. Two central concepts are arising: the unanticipated abundance of cis-antisense RNAs overlapping protein coding genes, and alternative transcripts resulting from a dynamic behaviour of operon structures (where genes can be included or excluded from a polycistronic transcript in response to environmental cues). Understanding these phenomena holds a great potential for our ability to decipher how bacteria regulate their complex life styles and pathogenic behaviours, but their dynamics, regulatory roles, and effects on combinatorially increasing the regulatory capacity of the genome are completely unknown.
The primary objectives of this proposed research are: i) to understand the extent, regulatory roles, and evolutionary consequences of cis-antisense
RNAs in prokaryotes; ii) to understand the regulatory code, combinatorial effects and dynamics of alternative operon structures; and, in parallel iii) to develop a unified framework for comparative prokaryotic transcriptomics.
Our strategy is based on a combination of deep sequencing technologies, computational modelling and data analyses, systems biology
approaches, and focused molecular biology experiments. We will identify the extent and the impact of these RNA-based regulatory layers in representative pathogenic and non-pathogenic species across the prokaryotic tree of life, study their functional and evolutionary consequences, and break the regulatory code controlling them. Our planned research has the potential of producing
methodological and conceptual breakthroughs in the emerging field of prokaryotic transcriptomics.
Max ERC Funding
1 499 540 €
Duration
Start date: 2011-01-01, End date: 2016-06-30
Project acronym SYMPAC
Project Synthetic metabolic pathways for carbon fixation
Researcher (PI) Ron Milo
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the principal reason for humanity s utilization of land and water. Under human cultivation, carbon fixation significantly limits growth. Hence increasing carbon fixation rate is of major importance towards agricultural and energetic sustainability.
Are there limits on the rate of such central metabolic pathways? Attempts to improve the rate of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved very limited success. In this proposal we try to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways utilizing the most effective carboxylating enzyme, PEPC. We propose to experimentally test these cycles in the most genetically tractable context by constructing an E. coli strain that will depend on carbon fixation as its sole carbon input. Energy will be supplied by compounds that cannot be used as carbon source. Initially, we will devise an autotrophic E. coli strain to use the Calvin-Benson Cycle; in the next stage, we will implement the most promising synthetic cycles. Systematic in vivo comparison will guide the future implementation in natural photosynthetic organisms.
At the basic science level, this proposal revisits and challenges our understanding of central carbon metabolism and growth. Concomitantly, it is an evolutionary experiment on integration of a biological novelty. It will serve as a model for significantly adapting a central metabolic pathway.
Summary
Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the principal reason for humanity s utilization of land and water. Under human cultivation, carbon fixation significantly limits growth. Hence increasing carbon fixation rate is of major importance towards agricultural and energetic sustainability.
Are there limits on the rate of such central metabolic pathways? Attempts to improve the rate of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved very limited success. In this proposal we try to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways utilizing the most effective carboxylating enzyme, PEPC. We propose to experimentally test these cycles in the most genetically tractable context by constructing an E. coli strain that will depend on carbon fixation as its sole carbon input. Energy will be supplied by compounds that cannot be used as carbon source. Initially, we will devise an autotrophic E. coli strain to use the Calvin-Benson Cycle; in the next stage, we will implement the most promising synthetic cycles. Systematic in vivo comparison will guide the future implementation in natural photosynthetic organisms.
At the basic science level, this proposal revisits and challenges our understanding of central carbon metabolism and growth. Concomitantly, it is an evolutionary experiment on integration of a biological novelty. It will serve as a model for significantly adapting a central metabolic pathway.
Max ERC Funding
1 498 792 €
Duration
Start date: 2011-01-01, End date: 2015-12-31
