Biochemistry (Hondele)Head of Research Unit Prof. Dr.Maria HondeleOverviewMembersPublicationsProjects & CollaborationsProjects & Collaborations OverviewMembersPublicationsProjects & Collaborations Projects & Collaborations 2 foundShow per page10 10 20 50 DDX TRANSIT Research Project | 1 Project MembersDEAD-box ATPases as master regulators of phase-separated compartments to control cellular RNA flux and the remodeling of RNA-protein complexes Life ultimately depends on the tight control of gene expression, which requires an ordered and efficient pro- cessing of various RNA molecules. Messenger RNAs (mRNAs) - bound by a constantly changing coat of passenger proteins - transit from transcription in the nucleus to translation and ultimately decay in the cyto- plasm. Similarly, ribosomal rRNAs migrate through the nucleolus where they gradually encounter ribosomal proteins to assemble functional ribosomes. Still, we know very little about the processes that orchestrate this flux of RNA in a temporal and spatial manner. Intriguingly, many RNA processing steps occur in membraneless organelles formed by liquid-liquid phase separation, e.g. nuclear speckles or the nucleolus, but the function of condensate formation in RNA pro- cessing is not known. I have discovered that the family of DEAD-box ATPases (DDXs) are master regula- tors of RNA-containing membraneless organelles, from bacteria to man. DDXs use their low-complexity domains and ATPase activity to regulate condensate dynamics and RNA flux through these compartments. I propose that cells use DDX-controlled condensate 'stations' to establish an RNA 'transit map' to reg- ulate the cellular flux of mRNA and rRNA molecules and to spatially and temporally control RNA processing. In three work packages, I will (1) characterize central DDXs that control mRNA flux and use DDX mutants as unique tools to map passenger protein changes along the life of an mRNA; (2) characterize how DDXs regulate the formation of the phase-separated nucleolar environment and facilitate the flux of rRNA during ribosome assembly; (3) dissect how DDX condensates function as biomolecular filters to selec- tively enrich or exclude proteins, and how selectivity contributes to the remodeling of the RNA protein coat and directional RNA flux. Our research will provide key novel insight into our understanding of RNA processing and uncover novel layers of gene expression regulation. The role of DEAD-box ATPases in the regulation of membraneless RNA organelles and spatio-temporal control of gene expression. Research Project | 2 Project MembersBackground: Gene expression is central to any process in life, and every (m)RNA processing step is tightly regulated by specific macromolecular complexes. However, we still know little how processing is orchestrated in a temporal and spatial manner, and how this affects gene expression. In recent years, the concept of liquid-liquid phase separation (LLPS) has revolutionized our understanding of molecular processes in cell biology: rapid and regulated formation of membraneless organelles reversibly compartmentalizes cellular components and creates highly dynamic biochemical reaction environments. During my postdoc, I discovered that bacterial, yeast and human RNA-dependent DEAD box ATPases (DDXs), abundant enzymes that chaperone every aspect of RNA life, undergo RNA-dependent LLPS in vitro and are critical regulators of membraneless organelle formation in vivo. These compartments control the accumulation of RNA molecules and selectively enrich for RNA processing factors. Rationale: I postulate that recruitment of RNA into DDX-compartments is a general, novel and conserved mechanism that controls the spatio-temporal flux of mRNA molecules between different steps of maturation and function. Objectives: Chaperoning mRNAs into phase-separated compartments opens up a novel layer of gene expression regulation, and in my future research, I want to study the molecular mechanisms, cellular function and universality of this phenomenon. Specific Aims: I will investigate how formation of two cytoplasmic DDX granules, P-bodies and stress granules, affects mRNA translation and turnover in vivo, and how DDX compartments influence remodelling of RNA-protein complexes in vitro. Moreover, I will probe the generality of my hypothesis and dissect which of the 65 human DDXs control formation of membraneless RNA compartments, how these enzymes are regulated by MIF4G domains, and quantify the influence of novel DDX compartments on gene expression. 1 1 OverviewMembersPublicationsProjects & Collaborations
Projects & Collaborations 2 foundShow per page10 10 20 50 DDX TRANSIT Research Project | 1 Project MembersDEAD-box ATPases as master regulators of phase-separated compartments to control cellular RNA flux and the remodeling of RNA-protein complexes Life ultimately depends on the tight control of gene expression, which requires an ordered and efficient pro- cessing of various RNA molecules. Messenger RNAs (mRNAs) - bound by a constantly changing coat of passenger proteins - transit from transcription in the nucleus to translation and ultimately decay in the cyto- plasm. Similarly, ribosomal rRNAs migrate through the nucleolus where they gradually encounter ribosomal proteins to assemble functional ribosomes. Still, we know very little about the processes that orchestrate this flux of RNA in a temporal and spatial manner. Intriguingly, many RNA processing steps occur in membraneless organelles formed by liquid-liquid phase separation, e.g. nuclear speckles or the nucleolus, but the function of condensate formation in RNA pro- cessing is not known. I have discovered that the family of DEAD-box ATPases (DDXs) are master regula- tors of RNA-containing membraneless organelles, from bacteria to man. DDXs use their low-complexity domains and ATPase activity to regulate condensate dynamics and RNA flux through these compartments. I propose that cells use DDX-controlled condensate 'stations' to establish an RNA 'transit map' to reg- ulate the cellular flux of mRNA and rRNA molecules and to spatially and temporally control RNA processing. In three work packages, I will (1) characterize central DDXs that control mRNA flux and use DDX mutants as unique tools to map passenger protein changes along the life of an mRNA; (2) characterize how DDXs regulate the formation of the phase-separated nucleolar environment and facilitate the flux of rRNA during ribosome assembly; (3) dissect how DDX condensates function as biomolecular filters to selec- tively enrich or exclude proteins, and how selectivity contributes to the remodeling of the RNA protein coat and directional RNA flux. Our research will provide key novel insight into our understanding of RNA processing and uncover novel layers of gene expression regulation. The role of DEAD-box ATPases in the regulation of membraneless RNA organelles and spatio-temporal control of gene expression. Research Project | 2 Project MembersBackground: Gene expression is central to any process in life, and every (m)RNA processing step is tightly regulated by specific macromolecular complexes. However, we still know little how processing is orchestrated in a temporal and spatial manner, and how this affects gene expression. In recent years, the concept of liquid-liquid phase separation (LLPS) has revolutionized our understanding of molecular processes in cell biology: rapid and regulated formation of membraneless organelles reversibly compartmentalizes cellular components and creates highly dynamic biochemical reaction environments. During my postdoc, I discovered that bacterial, yeast and human RNA-dependent DEAD box ATPases (DDXs), abundant enzymes that chaperone every aspect of RNA life, undergo RNA-dependent LLPS in vitro and are critical regulators of membraneless organelle formation in vivo. These compartments control the accumulation of RNA molecules and selectively enrich for RNA processing factors. Rationale: I postulate that recruitment of RNA into DDX-compartments is a general, novel and conserved mechanism that controls the spatio-temporal flux of mRNA molecules between different steps of maturation and function. Objectives: Chaperoning mRNAs into phase-separated compartments opens up a novel layer of gene expression regulation, and in my future research, I want to study the molecular mechanisms, cellular function and universality of this phenomenon. Specific Aims: I will investigate how formation of two cytoplasmic DDX granules, P-bodies and stress granules, affects mRNA translation and turnover in vivo, and how DDX compartments influence remodelling of RNA-protein complexes in vitro. Moreover, I will probe the generality of my hypothesis and dissect which of the 65 human DDXs control formation of membraneless RNA compartments, how these enzymes are regulated by MIF4G domains, and quantify the influence of novel DDX compartments on gene expression. 1 1
DDX TRANSIT Research Project | 1 Project MembersDEAD-box ATPases as master regulators of phase-separated compartments to control cellular RNA flux and the remodeling of RNA-protein complexes Life ultimately depends on the tight control of gene expression, which requires an ordered and efficient pro- cessing of various RNA molecules. Messenger RNAs (mRNAs) - bound by a constantly changing coat of passenger proteins - transit from transcription in the nucleus to translation and ultimately decay in the cyto- plasm. Similarly, ribosomal rRNAs migrate through the nucleolus where they gradually encounter ribosomal proteins to assemble functional ribosomes. Still, we know very little about the processes that orchestrate this flux of RNA in a temporal and spatial manner. Intriguingly, many RNA processing steps occur in membraneless organelles formed by liquid-liquid phase separation, e.g. nuclear speckles or the nucleolus, but the function of condensate formation in RNA pro- cessing is not known. I have discovered that the family of DEAD-box ATPases (DDXs) are master regula- tors of RNA-containing membraneless organelles, from bacteria to man. DDXs use their low-complexity domains and ATPase activity to regulate condensate dynamics and RNA flux through these compartments. I propose that cells use DDX-controlled condensate 'stations' to establish an RNA 'transit map' to reg- ulate the cellular flux of mRNA and rRNA molecules and to spatially and temporally control RNA processing. In three work packages, I will (1) characterize central DDXs that control mRNA flux and use DDX mutants as unique tools to map passenger protein changes along the life of an mRNA; (2) characterize how DDXs regulate the formation of the phase-separated nucleolar environment and facilitate the flux of rRNA during ribosome assembly; (3) dissect how DDX condensates function as biomolecular filters to selec- tively enrich or exclude proteins, and how selectivity contributes to the remodeling of the RNA protein coat and directional RNA flux. Our research will provide key novel insight into our understanding of RNA processing and uncover novel layers of gene expression regulation.
The role of DEAD-box ATPases in the regulation of membraneless RNA organelles and spatio-temporal control of gene expression. Research Project | 2 Project MembersBackground: Gene expression is central to any process in life, and every (m)RNA processing step is tightly regulated by specific macromolecular complexes. However, we still know little how processing is orchestrated in a temporal and spatial manner, and how this affects gene expression. In recent years, the concept of liquid-liquid phase separation (LLPS) has revolutionized our understanding of molecular processes in cell biology: rapid and regulated formation of membraneless organelles reversibly compartmentalizes cellular components and creates highly dynamic biochemical reaction environments. During my postdoc, I discovered that bacterial, yeast and human RNA-dependent DEAD box ATPases (DDXs), abundant enzymes that chaperone every aspect of RNA life, undergo RNA-dependent LLPS in vitro and are critical regulators of membraneless organelle formation in vivo. These compartments control the accumulation of RNA molecules and selectively enrich for RNA processing factors. Rationale: I postulate that recruitment of RNA into DDX-compartments is a general, novel and conserved mechanism that controls the spatio-temporal flux of mRNA molecules between different steps of maturation and function. Objectives: Chaperoning mRNAs into phase-separated compartments opens up a novel layer of gene expression regulation, and in my future research, I want to study the molecular mechanisms, cellular function and universality of this phenomenon. Specific Aims: I will investigate how formation of two cytoplasmic DDX granules, P-bodies and stress granules, affects mRNA translation and turnover in vivo, and how DDX compartments influence remodelling of RNA-protein complexes in vitro. Moreover, I will probe the generality of my hypothesis and dissect which of the 65 human DDXs control formation of membraneless RNA compartments, how these enzymes are regulated by MIF4G domains, and quantify the influence of novel DDX compartments on gene expression.
