Pub Date : 2021-02-17DOI: 10.1101/2021.02.17.431700
Mason Rouches, S. Veatch, B. Machta
Significance Proteins capable of separating into three-dimensional liquid droplets in the cytoplasm and nuclei of cells sometimes assemble in a two-dimensional form at membranes. These surface densities, enriched in specific proteins and lipids, often play decisive roles in cell signaling and membrane organization. Here a theoretical approach suggests that surface densities resemble prewet surface phases held together through a combination of two-dimensional membrane-mediated forces and three-dimensional protein interactions. The emergent physics of these liquid surface phases enable their roles both as dynamic scaffolds and as cooperative switches that propagate signals between the membrane and bulk. Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of animal cells appears tuned close to a two-dimensional liquid–liquid critical point. In some examples, cytoplasmic proteins aggregate at plasma membrane domains, forming structures such as the postsynaptic density and diverse signaling clusters. Here we examine the physics of these surface densities, employing minimal simulations of polymers prone to phase separation coupled to an Ising membrane surface in conjunction with a complementary Landau theory. We argue that these surface densities are a phase reminiscent of prewetting, in which a molecularly thin three-dimensional liquid forms on a usually solid surface. However, in surface densities the solid surface is replaced by a membrane with an independent propensity to phase separate. We show that proximity to criticality in the membrane dramatically increases the parameter regime in which a prewetting-like transition occurs, leading to a broad region where coexisting surface phases can form even when a bulk phase is unstable. Our simulations naturally exhibit three-surface phase coexistence even though both the membrane and the polymer bulk only display two-phase coexistence on their own. We argue that the physics of these surface densities may be shared with diverse functional structures seen in eukaryotic cells.
{"title":"Surface densities prewet a near-critical membrane","authors":"Mason Rouches, S. Veatch, B. Machta","doi":"10.1101/2021.02.17.431700","DOIUrl":"https://doi.org/10.1101/2021.02.17.431700","url":null,"abstract":"Significance Proteins capable of separating into three-dimensional liquid droplets in the cytoplasm and nuclei of cells sometimes assemble in a two-dimensional form at membranes. These surface densities, enriched in specific proteins and lipids, often play decisive roles in cell signaling and membrane organization. Here a theoretical approach suggests that surface densities resemble prewet surface phases held together through a combination of two-dimensional membrane-mediated forces and three-dimensional protein interactions. The emergent physics of these liquid surface phases enable their roles both as dynamic scaffolds and as cooperative switches that propagate signals between the membrane and bulk. Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of animal cells appears tuned close to a two-dimensional liquid–liquid critical point. In some examples, cytoplasmic proteins aggregate at plasma membrane domains, forming structures such as the postsynaptic density and diverse signaling clusters. Here we examine the physics of these surface densities, employing minimal simulations of polymers prone to phase separation coupled to an Ising membrane surface in conjunction with a complementary Landau theory. We argue that these surface densities are a phase reminiscent of prewetting, in which a molecularly thin three-dimensional liquid forms on a usually solid surface. However, in surface densities the solid surface is replaced by a membrane with an independent propensity to phase separate. We show that proximity to criticality in the membrane dramatically increases the parameter regime in which a prewetting-like transition occurs, leading to a broad region where coexisting surface phases can form even when a bulk phase is unstable. Our simulations naturally exhibit three-surface phase coexistence even though both the membrane and the polymer bulk only display two-phase coexistence on their own. We argue that the physics of these surface densities may be shared with diverse functional structures seen in eukaryotic cells.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85594693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-16DOI: 10.1101/2021.02.15.431339
S. A. Shuster, M. Wagner, Nathan Pan-Doh, Jing Ren, Sophie M. Grutzner, Kevin T. Beier, T. H. Kim, M. Schnitzer, L. Luo
Significance Cerebellar granule cells (GrCs) comprise the majority of all neurons in the mammalian brain and are usually regarded as a uniform cell type. However, the birth timing of individual GrCs dictates where their axons project. Using viral-genetic techniques, we find that early- and late-born GrCs receive different proportions of inputs from the same set of input regions. In vivo multidepth two-photon Ca2+ imaging of axons of early- and late-born GrCs reveals that both populations represent diverse task variables and stimuli, with small differences in the proportions of axons in encoding of a subset of movement and reward parameters. These results indicate that birth timing makes a modest contribution to the input selection and physiological response properties of GrCs. Cerebellar granule cells (GrCs) are usually regarded as a uniform cell type that collectively expands the coding space of the cerebellum by integrating diverse combinations of mossy fiber inputs. Accordingly, stable molecularly or physiologically defined GrC subtypes within a single cerebellar region have not been reported. The only known cellular property that distinguishes otherwise homogeneous GrCs is the correspondence between GrC birth timing and the depth of the molecular layer to which their axons project. To determine the role birth timing plays in GrC wiring and function, we developed genetic strategies to access early- and late-born GrCs. We initiated retrograde monosynaptic rabies virus tracing from control (birth timing unrestricted), early-born, and late-born GrCs, revealing the different patterns of mossy fiber input to GrCs in vermis lobule 6 and simplex, as well as to early- and late-born GrCs of vermis lobule 6: sensory and motor nuclei provide more input to early-born GrCs, while basal pontine and cerebellar nuclei provide more input to late-born GrCs. In vivo multidepth two-photon Ca2+ imaging of axons of early- and late-born GrCs revealed representations of diverse task variables and stimuli by both populations, with modest differences in the proportions encoding movement, reward anticipation, and reward consumption. Our results suggest neither organized parallel processing nor completely random organization of mossy fiber→GrC circuitry but instead a moderate influence of birth timing on GrC wiring and encoding. Our imaging data also provide evidence that GrCs can represent generalized responses to aversive stimuli, in addition to recently described reward representations.
{"title":"The relationship between birth timing, circuit wiring, and physiological response properties of cerebellar granule cells","authors":"S. A. Shuster, M. Wagner, Nathan Pan-Doh, Jing Ren, Sophie M. Grutzner, Kevin T. Beier, T. H. Kim, M. Schnitzer, L. Luo","doi":"10.1101/2021.02.15.431339","DOIUrl":"https://doi.org/10.1101/2021.02.15.431339","url":null,"abstract":"Significance Cerebellar granule cells (GrCs) comprise the majority of all neurons in the mammalian brain and are usually regarded as a uniform cell type. However, the birth timing of individual GrCs dictates where their axons project. Using viral-genetic techniques, we find that early- and late-born GrCs receive different proportions of inputs from the same set of input regions. In vivo multidepth two-photon Ca2+ imaging of axons of early- and late-born GrCs reveals that both populations represent diverse task variables and stimuli, with small differences in the proportions of axons in encoding of a subset of movement and reward parameters. These results indicate that birth timing makes a modest contribution to the input selection and physiological response properties of GrCs. Cerebellar granule cells (GrCs) are usually regarded as a uniform cell type that collectively expands the coding space of the cerebellum by integrating diverse combinations of mossy fiber inputs. Accordingly, stable molecularly or physiologically defined GrC subtypes within a single cerebellar region have not been reported. The only known cellular property that distinguishes otherwise homogeneous GrCs is the correspondence between GrC birth timing and the depth of the molecular layer to which their axons project. To determine the role birth timing plays in GrC wiring and function, we developed genetic strategies to access early- and late-born GrCs. We initiated retrograde monosynaptic rabies virus tracing from control (birth timing unrestricted), early-born, and late-born GrCs, revealing the different patterns of mossy fiber input to GrCs in vermis lobule 6 and simplex, as well as to early- and late-born GrCs of vermis lobule 6: sensory and motor nuclei provide more input to early-born GrCs, while basal pontine and cerebellar nuclei provide more input to late-born GrCs. In vivo multidepth two-photon Ca2+ imaging of axons of early- and late-born GrCs revealed representations of diverse task variables and stimuli by both populations, with modest differences in the proportions encoding movement, reward anticipation, and reward consumption. Our results suggest neither organized parallel processing nor completely random organization of mossy fiber→GrC circuitry but instead a moderate influence of birth timing on GrC wiring and encoding. Our imaging data also provide evidence that GrCs can represent generalized responses to aversive stimuli, in addition to recently described reward representations.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85988272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-13DOI: 10.1101/2021.02.12.431000
Stefan Schmollinger, Si Chen, Daniela Strenkert, Colleen Hui, M. Ralle, S. Merchant
Significance Transition metals are of crucial importance for primary productivity; their scarcity limits crop yield in agriculture and carbon sequestration on a global scale. Copper (Cu), iron (Fe), and manganese (Mn) are among the most important trace elements that enable the redox chemistry in oxygenic photosynthesis. The single-celled, eukaryotic green alga Chlamydomonas reinhardtii is a choice experimental system for studying trace metal homeostasis in the context of phototrophy, offering all the advantages of a classical microbial system with a well-characterized photosystem and trace metal metabolism machinery of relevance to plants. This project identifies and differentiates different trace metal storage sites in Chlamydomonas and uncovers the dynamics of trace metal storage and mobilization in situations of fluctuating resources. The acidocalcisome is an acidic organelle in the cytosol of eukaryotes, defined by its low pH and high calcium and polyphosphate content. It is visualized as an electron-dense object by transmission electron microscopy (TEM) or described with mass spectrometry (MS)–based imaging techniques or multimodal X-ray fluorescence microscopy (XFM) based on its unique elemental composition. Compared with MS-based imaging techniques, XFM offers the additional advantage of absolute quantification of trace metal content, since sectioning of the cell is not required and metabolic states can be preserved rapidly by either vitrification or chemical fixation. We employed XFM in Chlamydomonas reinhardtii to determine single-cell and organelle trace metal quotas within algal cells in situations of trace metal overaccumulation (Fe and Cu). We found up to 70% of the cellular Cu and 80% of Fe sequestered in acidocalcisomes in these conditions and identified two distinct populations of acidocalcisomes, defined by their unique trace elemental makeup. We utilized the vtc1 mutant, defective in polyphosphate synthesis and failing to accumulate Ca, to show that Fe sequestration is not dependent on either. Finally, quantitation of the Fe and Cu contents of individual cells and compartments via XFM, over a range of cellular metal quotas created by nutritional and genetic perturbations, indicated excellent correlation with bulk data from corresponding cell cultures, establishing a framework to distinguish the nutritional status of single cells.
{"title":"Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome-related organelles","authors":"Stefan Schmollinger, Si Chen, Daniela Strenkert, Colleen Hui, M. Ralle, S. Merchant","doi":"10.1101/2021.02.12.431000","DOIUrl":"https://doi.org/10.1101/2021.02.12.431000","url":null,"abstract":"Significance Transition metals are of crucial importance for primary productivity; their scarcity limits crop yield in agriculture and carbon sequestration on a global scale. Copper (Cu), iron (Fe), and manganese (Mn) are among the most important trace elements that enable the redox chemistry in oxygenic photosynthesis. The single-celled, eukaryotic green alga Chlamydomonas reinhardtii is a choice experimental system for studying trace metal homeostasis in the context of phototrophy, offering all the advantages of a classical microbial system with a well-characterized photosystem and trace metal metabolism machinery of relevance to plants. This project identifies and differentiates different trace metal storage sites in Chlamydomonas and uncovers the dynamics of trace metal storage and mobilization in situations of fluctuating resources. The acidocalcisome is an acidic organelle in the cytosol of eukaryotes, defined by its low pH and high calcium and polyphosphate content. It is visualized as an electron-dense object by transmission electron microscopy (TEM) or described with mass spectrometry (MS)–based imaging techniques or multimodal X-ray fluorescence microscopy (XFM) based on its unique elemental composition. Compared with MS-based imaging techniques, XFM offers the additional advantage of absolute quantification of trace metal content, since sectioning of the cell is not required and metabolic states can be preserved rapidly by either vitrification or chemical fixation. We employed XFM in Chlamydomonas reinhardtii to determine single-cell and organelle trace metal quotas within algal cells in situations of trace metal overaccumulation (Fe and Cu). We found up to 70% of the cellular Cu and 80% of Fe sequestered in acidocalcisomes in these conditions and identified two distinct populations of acidocalcisomes, defined by their unique trace elemental makeup. We utilized the vtc1 mutant, defective in polyphosphate synthesis and failing to accumulate Ca, to show that Fe sequestration is not dependent on either. Finally, quantitation of the Fe and Cu contents of individual cells and compartments via XFM, over a range of cellular metal quotas created by nutritional and genetic perturbations, indicated excellent correlation with bulk data from corresponding cell cultures, establishing a framework to distinguish the nutritional status of single cells.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"116 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91356854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-09DOI: 10.1101/2021.02.09.430509
Y. Hori, Justine C. Cléry, D. Schaeffer, Ravi S. Menon, S. Everling
Significance The common marmoset has enormous promise as a nonhuman primate model. While resting-state functional MRI (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. Here, we used movie-driven fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between marmoset monkeys and humans. The common marmoset has enormous promise as a nonhuman primate model of human brain functions. While resting-state functional MRI (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. This limitation can be overcome by movie-driven fMRI (md-fMRI), which has become a popular tool for noninvasively mapping the neural patterns generated by rich and naturalistic stimulation. Here, we used md-fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between New World marmoset monkeys and humans. However, while face patches in humans and marmosets were activated by marmoset faces, only human face patches responded to the faces of other animals. Together, the results demonstrate that higher-order visual processing might be a conserved feature between humans and New World marmoset monkeys but that small, potentially important functional differences exist.
{"title":"Interspecies activation correlations reveal functional correspondences between marmoset and human brain areas","authors":"Y. Hori, Justine C. Cléry, D. Schaeffer, Ravi S. Menon, S. Everling","doi":"10.1101/2021.02.09.430509","DOIUrl":"https://doi.org/10.1101/2021.02.09.430509","url":null,"abstract":"Significance The common marmoset has enormous promise as a nonhuman primate model. While resting-state functional MRI (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. Here, we used movie-driven fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between marmoset monkeys and humans. The common marmoset has enormous promise as a nonhuman primate model of human brain functions. While resting-state functional MRI (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. This limitation can be overcome by movie-driven fMRI (md-fMRI), which has become a popular tool for noninvasively mapping the neural patterns generated by rich and naturalistic stimulation. Here, we used md-fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between New World marmoset monkeys and humans. However, while face patches in humans and marmosets were activated by marmoset faces, only human face patches responded to the faces of other animals. Together, the results demonstrate that higher-order visual processing might be a conserved feature between humans and New World marmoset monkeys but that small, potentially important functional differences exist.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89204712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-09DOI: 10.1130/abs/2020am-352779
C. Lepre, P. Olsen
Significance Hematite provides much of the color for the classic Triassic–Jurassic “red beds” of North America and elsewhere. Measuring the spectrum of visible light reflected and absorbed by the red beds, we demonstrate that the hematite concentrations faithfully track 14.5 million years of Late Triassic monsoonal rainfall over the Colorado Plateau of Arizona and use this information to assess interrelationships between environmental perturbations, climate, and the evolution of terrestrial vertebrates. The research challenges conventional ideas that the hematite has limited use for interpreting the ancient past because it is a product of natural chemical alterations that occurred long after the beds were initially deposited. Hematite is the most abundant surficial iron oxide on Earth resulting from near-surface processes that make it important for addressing numerous geologic problems. While red beds have proved to be excellent paleomagnetic recorders, the early diagenetic origin of hematite in these units is often questioned. Here, we validate pigmentary hematite (“pigmentite”) as a proxy indicator for the Late Triassic environment and its penecontemporaneous origin by analyzing spectrophotometric measurements of a 14.5-My–long red bed sequence in scientific drill core CPCP-PFNP13-1A of the Chinle Formation, Arizona. Pigmentite concentrations in the red beds track the evolving pattern of the Late Triassic monsoon and indicate a long-term rise in aridity beginning at ∼215 Ma followed by increased oscillatory climate change at ∼213 Ma. These monsoonal changes are attributed to the northward drift of the Colorado Plateau as part of Laurentia into the arid subtropics during a time of fluctuating CO2. Our results refine the record of the Late Triassic monsoon and indicate significant changes in rainfall proximal to the Adamanian–Revueltian biotic transition that thus may have contributed to apparent faunal and floral events at 216 to 213 Ma.
{"title":"Hematite reconstruction of Late Triassic hydroclimate over the Colorado Plateau","authors":"C. Lepre, P. Olsen","doi":"10.1130/abs/2020am-352779","DOIUrl":"https://doi.org/10.1130/abs/2020am-352779","url":null,"abstract":"Significance Hematite provides much of the color for the classic Triassic–Jurassic “red beds” of North America and elsewhere. Measuring the spectrum of visible light reflected and absorbed by the red beds, we demonstrate that the hematite concentrations faithfully track 14.5 million years of Late Triassic monsoonal rainfall over the Colorado Plateau of Arizona and use this information to assess interrelationships between environmental perturbations, climate, and the evolution of terrestrial vertebrates. The research challenges conventional ideas that the hematite has limited use for interpreting the ancient past because it is a product of natural chemical alterations that occurred long after the beds were initially deposited. Hematite is the most abundant surficial iron oxide on Earth resulting from near-surface processes that make it important for addressing numerous geologic problems. While red beds have proved to be excellent paleomagnetic recorders, the early diagenetic origin of hematite in these units is often questioned. Here, we validate pigmentary hematite (“pigmentite”) as a proxy indicator for the Late Triassic environment and its penecontemporaneous origin by analyzing spectrophotometric measurements of a 14.5-My–long red bed sequence in scientific drill core CPCP-PFNP13-1A of the Chinle Formation, Arizona. Pigmentite concentrations in the red beds track the evolving pattern of the Late Triassic monsoon and indicate a long-term rise in aridity beginning at ∼215 Ma followed by increased oscillatory climate change at ∼213 Ma. These monsoonal changes are attributed to the northward drift of the Colorado Plateau as part of Laurentia into the arid subtropics during a time of fluctuating CO2. Our results refine the record of the Late Triassic monsoon and indicate significant changes in rainfall proximal to the Adamanian–Revueltian biotic transition that thus may have contributed to apparent faunal and floral events at 216 to 213 Ma.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77788794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-08DOI: 10.1101/2021.02.08.430262
Zhaleh Ghaemi, M. Gruebele, E. Tajkhorshid
Significance Hepatitis B virus (HBV) is a DNA virus that is 100 times more infectious than HIV. Despite the availability of a vaccine, the chronic infection rate of this virus is still over 250 million people globally. HBV chronic infection, for which no cure is currently available, can lead to liver cancer. Therefore, there is an unmet need to investigate the infection cycle of the virus. One of the most crucial steps in the virus-replication cycle is the release of its genetic material to the nucleus. During this step, the viral capsid enclosing the genetic material disassembles. However, its mechanism is unknown. Here, we utilize molecular simulations to shed light on the events leading to the capsid disassembly with atomistic detail. The disassembly of a viral capsid leading to the release of its genetic material into the host cell is a fundamental step in viral infection. In hepatitis B virus (HBV), the capsid consists of identical protein monomers that dimerize and then arrange themselves into pentamers or hexamers on the capsid surface. By applying atomistic molecular dynamics simulation to an entire solvated HBV capsid subjected to a uniform mechanical stress protocol, we monitor the capsid-disassembly process and analyze the process down to the level of individual amino acids in 20 independent simulation replicas. The strain of an isotropic external force, combined with structural fluctuations, causes structurally heterogeneous cracks to appear in the HBV capsid. Analysis of the monomer–monomer interfaces reveals that, in contrast to the expectation from purely mechanical considerations, the cracks mainly occur within hexameric sites, whereas pentameric sites remain largely intact. Only a small subset of the capsid protein monomers, different in each simulation, are engaged in each instance of disassembly. We identify specific residues whose interactions are most readily lost during disassembly; R127, I139, Y132, N136, A137, and V149 are among the hot spots at the interfaces between dimers that lie within hexamers, leading to disassembly. The majority of these hot-spot residues are conserved by evolution, hinting to their importance for disassembly by avoiding overstabilization of capsids.
{"title":"Molecular mechanism of capsid disassembly in hepatitis B virus","authors":"Zhaleh Ghaemi, M. Gruebele, E. Tajkhorshid","doi":"10.1101/2021.02.08.430262","DOIUrl":"https://doi.org/10.1101/2021.02.08.430262","url":null,"abstract":"Significance Hepatitis B virus (HBV) is a DNA virus that is 100 times more infectious than HIV. Despite the availability of a vaccine, the chronic infection rate of this virus is still over 250 million people globally. HBV chronic infection, for which no cure is currently available, can lead to liver cancer. Therefore, there is an unmet need to investigate the infection cycle of the virus. One of the most crucial steps in the virus-replication cycle is the release of its genetic material to the nucleus. During this step, the viral capsid enclosing the genetic material disassembles. However, its mechanism is unknown. Here, we utilize molecular simulations to shed light on the events leading to the capsid disassembly with atomistic detail. The disassembly of a viral capsid leading to the release of its genetic material into the host cell is a fundamental step in viral infection. In hepatitis B virus (HBV), the capsid consists of identical protein monomers that dimerize and then arrange themselves into pentamers or hexamers on the capsid surface. By applying atomistic molecular dynamics simulation to an entire solvated HBV capsid subjected to a uniform mechanical stress protocol, we monitor the capsid-disassembly process and analyze the process down to the level of individual amino acids in 20 independent simulation replicas. The strain of an isotropic external force, combined with structural fluctuations, causes structurally heterogeneous cracks to appear in the HBV capsid. Analysis of the monomer–monomer interfaces reveals that, in contrast to the expectation from purely mechanical considerations, the cracks mainly occur within hexameric sites, whereas pentameric sites remain largely intact. Only a small subset of the capsid protein monomers, different in each simulation, are engaged in each instance of disassembly. We identify specific residues whose interactions are most readily lost during disassembly; R127, I139, Y132, N136, A137, and V149 are among the hot spots at the interfaces between dimers that lie within hexamers, leading to disassembly. The majority of these hot-spot residues are conserved by evolution, hinting to their importance for disassembly by avoiding overstabilization of capsids.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89902698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-08DOI: 10.1101/2021.02.08.430233
Sarah K. Hu, Erica L. Herrera, Amy R. Smith, M. Pachiadaki, V. Edgcomb, S. Sylva, E. Chan, J. Seewald, C. German, J. Huber
Significance Heterotrophic protists are ubiquitous in all aquatic ecosystems and represent an important ecological link in food webs by transferring organic carbon from primary producers to higher trophic levels. Here, we quantify the predator–prey trophic interaction among protistan grazers and microbial prey within hydrothermal vent fluids from the Gorda Ridge spreading center in the northeast Pacific Ocean. Estimates of protistan grazing pressure were highest at sites of diffusely venting fluids, which are an oasis of biological activity in the deep sea. Our findings suggest that elevated grazing activity is attributed to a diverse assemblage of heterotrophic protistan species drawn to the hydrothermal vent habitat and demonstrates the important ecological roles that protists play in the deep-sea carbon cycle. Microbial eukaryotes (or protists) in marine ecosystems are a link between primary producers and all higher trophic levels, and the rate at which heterotrophic protistan grazers consume microbial prey is a key mechanism for carbon transport and recycling in microbial food webs. At deep-sea hydrothermal vents, chemosynthetic bacteria and archaea form the base of a food web that functions in the absence of sunlight, but the role of protistan grazers in these highly productive ecosystems is largely unexplored. Here, we pair grazing experiments with a molecular survey to quantify protistan grazing and to characterize the composition of vent-associated protists in low-temperature diffuse venting fluids from Gorda Ridge in the northeast Pacific Ocean. Results reveal protists exert higher predation pressure at vents compared to the surrounding deep seawater environment and may account for consuming 28 to 62% of the daily stock of prokaryotic biomass within discharging hydrothermal vent fluids. The vent-associated protistan community was more species rich relative to the background deep sea, and patterns in the distribution and co-occurrence of vent microbes provide additional insights into potential predator–prey interactions. Ciliates, followed by dinoflagellates, Syndiniales, rhizaria, and stramenopiles, dominated the vent protistan community and included bacterivorous species, species known to host symbionts, and parasites. Our findings provide an estimate of protistan grazing pressure within hydrothermal vent food webs, highlighting the important role that diverse protistan communities play in deep-sea carbon cycling.
{"title":"Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents","authors":"Sarah K. Hu, Erica L. Herrera, Amy R. Smith, M. Pachiadaki, V. Edgcomb, S. Sylva, E. Chan, J. Seewald, C. German, J. Huber","doi":"10.1101/2021.02.08.430233","DOIUrl":"https://doi.org/10.1101/2021.02.08.430233","url":null,"abstract":"Significance Heterotrophic protists are ubiquitous in all aquatic ecosystems and represent an important ecological link in food webs by transferring organic carbon from primary producers to higher trophic levels. Here, we quantify the predator–prey trophic interaction among protistan grazers and microbial prey within hydrothermal vent fluids from the Gorda Ridge spreading center in the northeast Pacific Ocean. Estimates of protistan grazing pressure were highest at sites of diffusely venting fluids, which are an oasis of biological activity in the deep sea. Our findings suggest that elevated grazing activity is attributed to a diverse assemblage of heterotrophic protistan species drawn to the hydrothermal vent habitat and demonstrates the important ecological roles that protists play in the deep-sea carbon cycle. Microbial eukaryotes (or protists) in marine ecosystems are a link between primary producers and all higher trophic levels, and the rate at which heterotrophic protistan grazers consume microbial prey is a key mechanism for carbon transport and recycling in microbial food webs. At deep-sea hydrothermal vents, chemosynthetic bacteria and archaea form the base of a food web that functions in the absence of sunlight, but the role of protistan grazers in these highly productive ecosystems is largely unexplored. Here, we pair grazing experiments with a molecular survey to quantify protistan grazing and to characterize the composition of vent-associated protists in low-temperature diffuse venting fluids from Gorda Ridge in the northeast Pacific Ocean. Results reveal protists exert higher predation pressure at vents compared to the surrounding deep seawater environment and may account for consuming 28 to 62% of the daily stock of prokaryotic biomass within discharging hydrothermal vent fluids. The vent-associated protistan community was more species rich relative to the background deep sea, and patterns in the distribution and co-occurrence of vent microbes provide additional insights into potential predator–prey interactions. Ciliates, followed by dinoflagellates, Syndiniales, rhizaria, and stramenopiles, dominated the vent protistan community and included bacterivorous species, species known to host symbionts, and parasites. Our findings provide an estimate of protistan grazing pressure within hydrothermal vent food webs, highlighting the important role that diverse protistan communities play in deep-sea carbon cycling.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"369 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73423100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dr. Takashi Sugimura: A giant of chemical carcinogenesis","authors":"J. Trosko","doi":"10.1073/pnas.2021938118","DOIUrl":"https://doi.org/10.1073/pnas.2021938118","url":null,"abstract":"","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88647188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-07DOI: 10.1101/2021.02.06.430010
Zhangqiang Li, Xueqin Jin, Tong Wu, Xin Zhao, Weipeng Wang, Jianlin Lei, Xiaojing Pan, N. Yan
Significance Dysfunction of Nav1.5, the primary cardiac Nav channel, is associated with multiple arrhythmia syndromes, exemplified by type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). Establishment of the structure-function relationship and mechanistic understanding of the disease variants will facilitate the development of antiarrhythmic drugs. Here we report the cryo-EM structure of human Nav1.5-E1784K, the most common variant shared by LQT3 and BrS. Structural mapping of 91 LQT3-associated mutations reveal a hotspot that involves the fast inactivation segments. The high density of LQT3 mutation sites in this region can be reasonably interpreted by the “door wedge” model for fast inactivation, which was derived from our previous structural observations and is supported by a wealth of functional characterizations. Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 Å. The structure is nearly identical to that of the wild-type human Nav1.5 bound to quinidine. Structural mapping of 91- and 178-point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are clustered mainly to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our “door wedge” model for fast inactivation. The structural analysis presented here, with a focus on the impact of mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.
{"title":"Structure of human Nav1.5 reveals the fast inactivation-related segments as a mutational hotspot for the long QT syndrome","authors":"Zhangqiang Li, Xueqin Jin, Tong Wu, Xin Zhao, Weipeng Wang, Jianlin Lei, Xiaojing Pan, N. Yan","doi":"10.1101/2021.02.06.430010","DOIUrl":"https://doi.org/10.1101/2021.02.06.430010","url":null,"abstract":"Significance Dysfunction of Nav1.5, the primary cardiac Nav channel, is associated with multiple arrhythmia syndromes, exemplified by type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). Establishment of the structure-function relationship and mechanistic understanding of the disease variants will facilitate the development of antiarrhythmic drugs. Here we report the cryo-EM structure of human Nav1.5-E1784K, the most common variant shared by LQT3 and BrS. Structural mapping of 91 LQT3-associated mutations reveal a hotspot that involves the fast inactivation segments. The high density of LQT3 mutation sites in this region can be reasonably interpreted by the “door wedge” model for fast inactivation, which was derived from our previous structural observations and is supported by a wealth of functional characterizations. Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 Å. The structure is nearly identical to that of the wild-type human Nav1.5 bound to quinidine. Structural mapping of 91- and 178-point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are clustered mainly to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our “door wedge” model for fast inactivation. The structural analysis presented here, with a focus on the impact of mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87318925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-02DOI: 10.1101/2021.02.02.429360
Patrick J. Flynn, P. Koch, T. Mitchison
Significance Cancer chemotherapeutic drugs that induce mitotic errors may cause tumor regression in part through the induction of interferon signaling. To test this idea, we measured the ability of antimitotic drugs with different mechanisms to activate the cGAS–STING–interferon pathway. Only microtubule stabilizers and MPS1 inhibitors activated cGAS, and this correlated with their ability to generate cGAS-coated chromatin bridges. We propose that chromatin bridges activate cGAS through a tension-dependent mechanism that depends on cytokinesis. Our results may explain the clinical failure of antimitotic drugs and help to design improved drugs. Mitotic errors can activate cyclic GMP–AMP synthase (cGAS) and induce type I interferon (IFN) signaling. Current models propose that chromosome segregation errors generate micronuclei whose rupture activates cGAS. We used a panel of antimitotic drugs to perturb mitosis in human fibroblasts and measured abnormal nuclear morphologies, cGAS localization, and IFN signaling in the subsequent interphase. Micronuclei consistently recruited cGAS without activating it. Instead, IFN signaling correlated with formation of cGAS-coated chromatin bridges that were selectively generated by microtubule stabilizers and MPS1 inhibitors. cGAS activation by chromatin bridges was suppressed by drugs that prevented cytokinesis. We confirmed cGAS activation by chromatin bridges in cancer lines that are unable to secrete IFN by measuring paracrine transfer of 2′3′-cGAMP to fibroblasts, and in mouse cells. We propose that cGAS is selectively activated by self-chromatin when it is stretched in chromatin bridges. Immunosurveillance of cells that fail mitosis, and antitumor actions of taxanes and MPS1 inhibitors, may depend on this effect.
{"title":"Chromatin bridges, not micronuclei, activate cGAS after drug-induced mitotic errors in human cells","authors":"Patrick J. Flynn, P. Koch, T. Mitchison","doi":"10.1101/2021.02.02.429360","DOIUrl":"https://doi.org/10.1101/2021.02.02.429360","url":null,"abstract":"Significance Cancer chemotherapeutic drugs that induce mitotic errors may cause tumor regression in part through the induction of interferon signaling. To test this idea, we measured the ability of antimitotic drugs with different mechanisms to activate the cGAS–STING–interferon pathway. Only microtubule stabilizers and MPS1 inhibitors activated cGAS, and this correlated with their ability to generate cGAS-coated chromatin bridges. We propose that chromatin bridges activate cGAS through a tension-dependent mechanism that depends on cytokinesis. Our results may explain the clinical failure of antimitotic drugs and help to design improved drugs. Mitotic errors can activate cyclic GMP–AMP synthase (cGAS) and induce type I interferon (IFN) signaling. Current models propose that chromosome segregation errors generate micronuclei whose rupture activates cGAS. We used a panel of antimitotic drugs to perturb mitosis in human fibroblasts and measured abnormal nuclear morphologies, cGAS localization, and IFN signaling in the subsequent interphase. Micronuclei consistently recruited cGAS without activating it. Instead, IFN signaling correlated with formation of cGAS-coated chromatin bridges that were selectively generated by microtubule stabilizers and MPS1 inhibitors. cGAS activation by chromatin bridges was suppressed by drugs that prevented cytokinesis. We confirmed cGAS activation by chromatin bridges in cancer lines that are unable to secrete IFN by measuring paracrine transfer of 2′3′-cGAMP to fibroblasts, and in mouse cells. We propose that cGAS is selectively activated by self-chromatin when it is stretched in chromatin bridges. Immunosurveillance of cells that fail mitosis, and antitumor actions of taxanes and MPS1 inhibitors, may depend on this effect.","PeriodicalId":20595,"journal":{"name":"Proceedings of the National Academy of Sciences","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83000934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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