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Mitochondria and Memory: Bioenergetics, Synaptic Plasticity and Neurodegeneration
180a
Monday, February 13, 2017
appears to be the maintenance of organized inner membrane invaginations. In parallel, we have shown that the proteins of the respiratory chain are located in the flat membrane regions of cristae and that they form species specific super˚ struccomplexes. Alongside the cryo-ET studies, we have determined a 6.2A ture of the mitochondrial ATP synthase of Polytomella sp. using single particle cryo-EM. Our structure revealed four highly tilted membraneintrinsic helices (~20 to the membrane plane) adjacent to the rotor ring which we assign to the elusive a-subunit. Based on this structure, we present a model describing how protons move through the ATP synthase. 888-Symp Mitochondria and Memory: Bioenergetics, Synaptic Plasticity and Neurodegeneration Elizabeth A. Jonas1, Nelli Mnatsakanyan1, Paige Miranda1, Han-A Park1, Rongmin Chen1, Pawel Licznerski1, Maria Weinert2, Peter J.S. Smith3, Andres Chavez4, R Suzanne Zukin4, Valentin K. Gribkoff1, Kambiz N. Alavian2. 1 Yale University, New Haven, CT, USA, 2Imperial College, London, United Kingdom, 3University of Southampton, Southampton, United Kingdom, 4 Albert Einstein, New York, NY, USA. Mitochondrial and synaptic dysfunction occur in neurodegenerative disease. Preservation of the physiological ability of a synapse to alter the frequency or amplitude of its responses after changes in activity level appears to be required for normal brain function; failure to attain healthy synaptic plasticity underlies deficits in diverse brain diseases. The cell death channel known as the mitochondrial permeability transition pore (mPTP) is likely to be an important therapeutic target in neurodegeneration but whether mPTP in the synapse contributes to mitochondrial and synaptic plasticity has yet to be explored. We hypothesized that changes in the probability of opening of mPTP may participate in long lasting changes to mitochondria during changes in synaptic efficacy. We now find that molecules such as the anti-apoptotic protein Bcl-xL and the protein DJ1 that is necessary to prevent Parkinson’s Disease contribute to enhancing mitochondrial efficiency; these proteins move to mitochondria from the cytosol upon neuronal stimulation. Interaction of Bcl-xL and DJ1 with the ATP synthase F1 catalytic domain increases the probability of closure of a voltage dependent c-subunit leak channel, a candidate for the mPTP on which we have recently reported. Translocation of BclxL or DJ1 is associated with long lasting increases in production of ATP by mitochondria at synaptic sites. We therefore suggest a physiological, prosynaptic, role for mPTP during synaptic plasticity: Our studies suggest that an acute change in mitochondrial efficiency brought on by closure of mPTP is required for the establishment of long term potentiation of synaptic transmission. We are now investigating the mechanism by which Bcl-xL- and DJ1-regulated metabolic changes support synaptic plasticity and how this becomes dysfunctional in neurodegenerative models. We hope that our findings may lead to the design of specific therapeutic compounds to target mPTP directly, attenuating neurodegeneration.
Symposium: Epigenomic Changes Driven by Biomechanical Load 889-Symp Systems Mechanobiology of Cardiac Myocytes Andrew D. McCulloch. Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA. Cardiac myocytes are sensitive to specific and distinct mechanical stimuli. We examined the effect of the major axis of biaxial mechanical stretch on cardiac myocyte gene expression and reconstructed a stretch signaling model to identify pathways and transcription factors regulating these responses. Neonatal cardiac myocytes were cultured on a micropatterned substrate, and the primary stretch axis was applied either parallel or transverse to the myofibril direction. RNA sequencing (RNA-Seq) after acute myocyte stretch showed a more robust response to longitudinal than to transverse stretch. After 30 minutes of stretch, 53 and 168 genes were significantly up- or down-regulated by transverse or longitudinal stretch, respectively. After 4 hours, the number of differentially expressed genes increased to 795 with longitudinal stretch but only 35 with transverse stretch. Genes regulated by both stretches showed significant enrichment of transcription factor activity and protein kinase activity, whereas longitudinal but not transverse stretch specifically activated genes involved in sarcomere organization and cytoskeletal protein binding. Network analysis using logic-based signaling model constructed from published data identified serum response factor (SRF) and myocyte enhancer factor-2 (MEF2) as critical regulators of longitudinal stretch-induced changes mediated by protein kinase C (PKC).
cAMP response element-binding protein (CREB) was found to be activated by both longitudinal and transverse stretch. Inhibitor experiments were used to validate these model predictions. Cardiac myocytes activate different pathways in response to transverse and longitudinal mechanical strain; these responses may underlie differential whole organ responses to pressure versus volume overload. 890-Symp The ‘‘Self-Stirred’’ Genome: Bulk and Surface Dynamics of the Chromatin Globule Alexandra Zidovska. Department of Physics, New York University, New York, NY, USA. Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood. In interphase, time between two cell divisions, chromatin fills the cell nucleus in its minimally condensed polymeric state. Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured. These are energy-consuming processes giving rise to non-equilibrium dynamics. Chromatin dynamics has been traditionally studied by imaging of fluorescently labeled nuclear proteins and single DNA-sites, thus focusing only on a small number of tracer particles. Recently, we developed an approach, displacement correlation spectroscopy (DCS) based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells [1]. DCS revealed that chromatin movement was coherent across large regions (4–5mm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes [1]. These large-scale, coupled motions were ATP-dependent and unidirectional for several seconds. Following these observations, we developed a hydrodynamic theory of active chromatin dynamics, using the two-fluid model and describing the content of cell nucleus as a chromatin solution, which is subject to both passive thermal fluctuations and active (ATP-consuming) scalar and vector events [2]. In this work we continue in our efforts to elucidate the mechanism and function of the chromatin dynamics in interphase. We investigate the chromatin interactions with the nuclear envelope and compare the surface dynamics of the chromatin globule with its bulk dynamics. [1] Zidovska A, Weitz DA, Mitchison TJ, PNAS, 110 (39), 15555, 2013 [2] Bruinsma R, Grosberg AY, Rabin Y, Zidovska A, Biophys. J., 106 (9), 1871, 2014 891-Symp Epigenetic Regulation of Chromatin Dynamics Michael G. Poirier. Physics, Ohio State Universtiy, Columbus, OH, USA. The physical organization of all eukaryotic genomes is evolutionarily conserved where octamers of histone proteins repeatedly wrap DNA into nucleosomes to form long chromatin fibers. Post translational modifications (PTMs) of histone protein octamers regulate essential DNA processing, including RNA transcription and DNA repair. I will discuss our recent work to understand how histone PTMs, and the proteins that bind these PTMs, combine to regulate DNA accessibility to transcription regulatory complexes through controlling chromatin structural dynamics. 892-Symp Multi-Scale Modeling of Chromosomal DNA in Prokaryotic and Eukaryotic Cells Andrew J. Spakowitz. Chemical Engineering, Stanford University, Stanford, CA, USA. The organization and dynamics of chromosomal DNA play a pivotal role in a range of biological processes, including gene regulation, homologous recombination, replication, and segregation. Establishing a quantitative theoretical model of DNA organization and dynamics would be valuable in bridging the gap between the molecular-level packaging of DNA and genome-scale chromosomal processes. Our research group utilizes analytical theory and computational modeling to establish a predictive theoretical model of chromosomal organization and dynamics. In this talk, I will discuss our efforts to develop multi-scale polymer models of chromosomal DNA that are both sufficiently detailed to address specific protein-DNA interactions while capturing experimentally relevant time and length scales. I will demonstrate how these modeling efforts are capable of quantitatively capturing aspects of behavior of chromosomal DNA in both prokaryotic and eukaryotic cells. This talk will illustrate that capturing dynamical behavior of chromosomal DNA at various length scales necessitates a range of theoretical treatments that accommodate the critical physical contributions that are relevant to in vivo behavior at these disparate length and time scales.
Monday, February 13, 2017
appears to be the maintenance of organized inner membrane invaginations. In parallel, we have shown that the proteins of the respiratory chain are located in the flat membrane regions of cristae and that they form species specific super˚ struccomplexes. Alongside the cryo-ET studies, we have determined a 6.2A ture of the mitochondrial ATP synthase of Polytomella sp. using single particle cryo-EM. Our structure revealed four highly tilted membraneintrinsic helices (~20 to the membrane plane) adjacent to the rotor ring which we assign to the elusive a-subunit. Based on this structure, we present a model describing how protons move through the ATP synthase. 888-Symp Mitochondria and Memory: Bioenergetics, Synaptic Plasticity and Neurodegeneration Elizabeth A. Jonas1, Nelli Mnatsakanyan1, Paige Miranda1, Han-A Park1, Rongmin Chen1, Pawel Licznerski1, Maria Weinert2, Peter J.S. Smith3, Andres Chavez4, R Suzanne Zukin4, Valentin K. Gribkoff1, Kambiz N. Alavian2. 1 Yale University, New Haven, CT, USA, 2Imperial College, London, United Kingdom, 3University of Southampton, Southampton, United Kingdom, 4 Albert Einstein, New York, NY, USA. Mitochondrial and synaptic dysfunction occur in neurodegenerative disease. Preservation of the physiological ability of a synapse to alter the frequency or amplitude of its responses after changes in activity level appears to be required for normal brain function; failure to attain healthy synaptic plasticity underlies deficits in diverse brain diseases. The cell death channel known as the mitochondrial permeability transition pore (mPTP) is likely to be an important therapeutic target in neurodegeneration but whether mPTP in the synapse contributes to mitochondrial and synaptic plasticity has yet to be explored. We hypothesized that changes in the probability of opening of mPTP may participate in long lasting changes to mitochondria during changes in synaptic efficacy. We now find that molecules such as the anti-apoptotic protein Bcl-xL and the protein DJ1 that is necessary to prevent Parkinson’s Disease contribute to enhancing mitochondrial efficiency; these proteins move to mitochondria from the cytosol upon neuronal stimulation. Interaction of Bcl-xL and DJ1 with the ATP synthase F1 catalytic domain increases the probability of closure of a voltage dependent c-subunit leak channel, a candidate for the mPTP on which we have recently reported. Translocation of BclxL or DJ1 is associated with long lasting increases in production of ATP by mitochondria at synaptic sites. We therefore suggest a physiological, prosynaptic, role for mPTP during synaptic plasticity: Our studies suggest that an acute change in mitochondrial efficiency brought on by closure of mPTP is required for the establishment of long term potentiation of synaptic transmission. We are now investigating the mechanism by which Bcl-xL- and DJ1-regulated metabolic changes support synaptic plasticity and how this becomes dysfunctional in neurodegenerative models. We hope that our findings may lead to the design of specific therapeutic compounds to target mPTP directly, attenuating neurodegeneration.
Symposium: Epigenomic Changes Driven by Biomechanical Load 889-Symp Systems Mechanobiology of Cardiac Myocytes Andrew D. McCulloch. Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA. Cardiac myocytes are sensitive to specific and distinct mechanical stimuli. We examined the effect of the major axis of biaxial mechanical stretch on cardiac myocyte gene expression and reconstructed a stretch signaling model to identify pathways and transcription factors regulating these responses. Neonatal cardiac myocytes were cultured on a micropatterned substrate, and the primary stretch axis was applied either parallel or transverse to the myofibril direction. RNA sequencing (RNA-Seq) after acute myocyte stretch showed a more robust response to longitudinal than to transverse stretch. After 30 minutes of stretch, 53 and 168 genes were significantly up- or down-regulated by transverse or longitudinal stretch, respectively. After 4 hours, the number of differentially expressed genes increased to 795 with longitudinal stretch but only 35 with transverse stretch. Genes regulated by both stretches showed significant enrichment of transcription factor activity and protein kinase activity, whereas longitudinal but not transverse stretch specifically activated genes involved in sarcomere organization and cytoskeletal protein binding. Network analysis using logic-based signaling model constructed from published data identified serum response factor (SRF) and myocyte enhancer factor-2 (MEF2) as critical regulators of longitudinal stretch-induced changes mediated by protein kinase C (PKC).
cAMP response element-binding protein (CREB) was found to be activated by both longitudinal and transverse stretch. Inhibitor experiments were used to validate these model predictions. Cardiac myocytes activate different pathways in response to transverse and longitudinal mechanical strain; these responses may underlie differential whole organ responses to pressure versus volume overload. 890-Symp The ‘‘Self-Stirred’’ Genome: Bulk and Surface Dynamics of the Chromatin Globule Alexandra Zidovska. Department of Physics, New York University, New York, NY, USA. Chromatin structure and dynamics control all aspects of DNA biology yet are poorly understood. In interphase, time between two cell divisions, chromatin fills the cell nucleus in its minimally condensed polymeric state. Chromatin serves as substrate to a number of biological processes, e.g. gene expression and DNA replication, which require it to become locally restructured. These are energy-consuming processes giving rise to non-equilibrium dynamics. Chromatin dynamics has been traditionally studied by imaging of fluorescently labeled nuclear proteins and single DNA-sites, thus focusing only on a small number of tracer particles. Recently, we developed an approach, displacement correlation spectroscopy (DCS) based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells [1]. DCS revealed that chromatin movement was coherent across large regions (4–5mm) for several seconds. Regions of coherent motion extended beyond the boundaries of single-chromosome territories, suggesting elastic coupling of motion over length scales much larger than those of genes [1]. These large-scale, coupled motions were ATP-dependent and unidirectional for several seconds. Following these observations, we developed a hydrodynamic theory of active chromatin dynamics, using the two-fluid model and describing the content of cell nucleus as a chromatin solution, which is subject to both passive thermal fluctuations and active (ATP-consuming) scalar and vector events [2]. In this work we continue in our efforts to elucidate the mechanism and function of the chromatin dynamics in interphase. We investigate the chromatin interactions with the nuclear envelope and compare the surface dynamics of the chromatin globule with its bulk dynamics. [1] Zidovska A, Weitz DA, Mitchison TJ, PNAS, 110 (39), 15555, 2013 [2] Bruinsma R, Grosberg AY, Rabin Y, Zidovska A, Biophys. J., 106 (9), 1871, 2014 891-Symp Epigenetic Regulation of Chromatin Dynamics Michael G. Poirier. Physics, Ohio State Universtiy, Columbus, OH, USA. The physical organization of all eukaryotic genomes is evolutionarily conserved where octamers of histone proteins repeatedly wrap DNA into nucleosomes to form long chromatin fibers. Post translational modifications (PTMs) of histone protein octamers regulate essential DNA processing, including RNA transcription and DNA repair. I will discuss our recent work to understand how histone PTMs, and the proteins that bind these PTMs, combine to regulate DNA accessibility to transcription regulatory complexes through controlling chromatin structural dynamics. 892-Symp Multi-Scale Modeling of Chromosomal DNA in Prokaryotic and Eukaryotic Cells Andrew J. Spakowitz. Chemical Engineering, Stanford University, Stanford, CA, USA. The organization and dynamics of chromosomal DNA play a pivotal role in a range of biological processes, including gene regulation, homologous recombination, replication, and segregation. Establishing a quantitative theoretical model of DNA organization and dynamics would be valuable in bridging the gap between the molecular-level packaging of DNA and genome-scale chromosomal processes. Our research group utilizes analytical theory and computational modeling to establish a predictive theoretical model of chromosomal organization and dynamics. In this talk, I will discuss our efforts to develop multi-scale polymer models of chromosomal DNA that are both sufficiently detailed to address specific protein-DNA interactions while capturing experimentally relevant time and length scales. I will demonstrate how these modeling efforts are capable of quantitatively capturing aspects of behavior of chromosomal DNA in both prokaryotic and eukaryotic cells. This talk will illustrate that capturing dynamical behavior of chromosomal DNA at various length scales necessitates a range of theoretical treatments that accommodate the critical physical contributions that are relevant to in vivo behavior at these disparate length and time scales.