ABSTRACT
Human cytomegalovirus (HCMV) infects the majority of the human population and represents the leading viral cause of congenital birth defects. HCMV utilizes the glycoproteins gHgLgO (Trimer) to bind to platelet-derived growth factor receptor alpha (PDGFRα) and transforming growth factor beta receptor 3 (TGFßR3) to gain entry into multiple cell types. This complex is targeted by potent neutralizing antibodies and represents an important candidate for therapeutics against HCMV. Here, we determine three cryogenic electron microscopy (cryo-EM) structures of the trimer and the details of its interactions with four binding partners: the receptor proteins PDGFRα and TGFßR3 as well as two broadly neutralizing antibodies. Trimer binding to PDGFRα and TGFßR3 is mutually exclusive, suggesting that they function as independent entry receptors. In addition, Trimer-PDGFRα interaction has an inhibitory effect on PDGFRα signaling. Our results provide a framework for understanding HCMV receptor engagement, neutralization, and the development of anti-viral strategies against HCMV.
Subject(s)
Cytomegalovirus/chemistry , Membrane Glycoproteins/chemistry , Viral Envelope Proteins/chemistry , Virus Internalization , Cryoelectron Microscopy , Cytomegalovirus/physiology , Membrane Glycoproteins/metabolism , Models, Molecular , Proteoglycans/metabolism , Receptor, Platelet-Derived Growth Factor alpha/chemistry , Receptor, Platelet-Derived Growth Factor alpha/metabolism , Receptors, Transforming Growth Factor beta/metabolism , Viral Envelope Proteins/metabolismABSTRACT
Lymphocyte migration is essential for adaptive immune surveillance. However, our current understanding of this process is rudimentary, because most human studies have been restricted to immunological analyses of blood and various tissues. To address this knowledge gap, we used an integrated approach to characterize tissue-emigrant lineages in thoracic duct lymph (TDL). The most prevalent immune cells in human and non-human primate efferent lymph were T cells. Cytolytic CD8+ T cell subsets with effector-like epigenetic and transcriptional signatures were clonotypically skewed and selectively confined to the intravascular circulation, whereas non-cytolytic CD8+ T cell subsets with stem-like epigenetic and transcriptional signatures predominated in tissues and TDL. Moreover, these anatomically distinct gene expression profiles were recapitulated within individual clonotypes, suggesting parallel differentiation programs independent of the expressed antigen receptor. Our collective dataset provides an atlas of the migratory immune system and defines the nature of tissue-emigrant CD8+ T cells that recirculate via TDL.
Subject(s)
CD8-Positive T-Lymphocytes/cytology , CD8-Positive T-Lymphocytes/immunology , Animals , Cell Differentiation , Clone Cells , Cytotoxicity, Immunologic , Epigenesis, Genetic , Humans , Immunologic Memory , Lymph Nodes/cytology , Lymph Nodes/immunology , Macaca mulatta , T-Lymphocyte Subsets/immunology , Transcription, Genetic , Transcriptome/geneticsABSTRACT
Activated T cells differentiate into functional subsets with distinct metabolic programs. Glutaminase (GLS) converts glutamine to glutamate to support the tricarboxylic acid cycle and redox and epigenetic reactions. Here, we identify a key role for GLS in T cell activation and specification. Though GLS deficiency diminished initial T cell activation and proliferation and impaired differentiation of Th17 cells, loss of GLS also increased Tbet to promote differentiation and effector function of CD4 Th1 and CD8 CTL cells. This was associated with altered chromatin accessibility and gene expression, including decreased PIK3IP1 in Th1 cells that sensitized to IL-2-mediated mTORC1 signaling. In vivo, GLS null T cells failed to drive Th17-inflammatory diseases, and Th1 cells had initially elevated function but exhausted over time. Transient GLS inhibition, however, led to increased Th1 and CTL T cell numbers. Glutamine metabolism thus has distinct roles to promote Th17 but constrain Th1 and CTL effector cell differentiation.
Subject(s)
CD8-Positive T-Lymphocytes/immunology , Cell Differentiation/immunology , Glutaminase/immunology , Lymphocyte Activation , Th1 Cells/immunology , Th17 Cells/immunology , Animals , CD8-Positive T-Lymphocytes/cytology , Cell Differentiation/genetics , Glutaminase/genetics , Male , Mice , Mice, Transgenic , Th1 Cells/cytology , Th17 Cells/cytologyABSTRACT
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
Subject(s)
Evolution, Molecular , Homeodomain Proteins , Locomotion , Marsupialia , Transcription Factors , Animals , Female , Male , Mice , Epigenomics , Gene Expression Profiling , Gene Expression Regulation, Developmental , Genome/genetics , Genomics , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Locomotion/genetics , Marsupialia/anatomy & histology , Marsupialia/classification , Marsupialia/genetics , Marsupialia/growth & development , Phylogeny , Regulatory Sequences, Nucleic Acid/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Phenotype , HumansABSTRACT
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
Subject(s)
Evolution, Molecular , Genes, Plant , Genomics , Magnoliopsida , Phylogeny , Fossils , Genes, Plant/genetics , Magnoliopsida/genetics , Magnoliopsida/classification , Nuclear Proteins/geneticsABSTRACT
CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity, bacteriophages have evolved diverse families of anti-CRISPR proteins (Acrs). Recently, Lin et al. (2020) described the discovery and characterization of 7 Acr families (AcrVIA1-7) that inhibit type VI-A CRISPR systems. We detail several inconsistencies that question the results reported in the Lin et al. (2020) study. These include inaccurate bioinformatics analyses and bacterial strains that are impossible to construct. Published strains were provided by the authors, but MS2 bacteriophage plaque assays did not support the published results. We also independently tested the Acr sequences described in the original report, in E. coli and mammalian cells, but did not observe anti-Cas13a activity. Taken together, our data and analyses prompt us to question the claim that AcrVIA1-7 reported in Lin et al. are type VI anti-CRISPR proteins.
Subject(s)
Bacteriophages , CRISPR-Associated Proteins , Animals , Bacteriophages/genetics , CRISPR-Associated Proteins/genetics , CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems , Escherichia coli/genetics , Escherichia coli/metabolism , Leptotrichia/genetics , Mammals/metabolism , Prophages/genetics , Prophages/metabolism , Ribonucleases/metabolismABSTRACT
Plasma membrane rupture (PMR) in dying cells undergoing pyroptosis or apoptosis requires the cell-surface protein NINJ11. PMR releases pro-inflammatory cytoplasmic molecules, collectively called damage-associated molecular patterns (DAMPs), that activate immune cells. Therefore, inhibiting NINJ1 and PMR may limit the inflammation that is associated with excessive cell death. Here we describe an anti-NINJ1 monoclonal antibody that specifically targets mouse NINJ1 and blocks oligomerization of NINJ1, preventing PMR. Electron microscopy studies showed that this antibody prevents NINJ1 from forming oligomeric filaments. In mice, inhibition of NINJ1 or Ninj1 deficiency ameliorated hepatocellular PMR induced with TNF plus D-galactosamine, concanavalin A, Jo2 anti-Fas agonist antibody or ischaemia-reperfusion injury. Accordingly, serum levels of lactate dehydrogenase, the liver enzymes alanine aminotransaminase and aspartate aminotransferase, and the DAMPs interleukin 18 and HMGB1 were reduced. Moreover, in the liver ischaemia-reperfusion injury model, there was an attendant reduction in neutrophil infiltration. These data indicate that NINJ1 mediates PMR and inflammation in diseases driven by aberrant hepatocellular death.
Subject(s)
Antibodies, Monoclonal , Cell Membrane , Inflammation , Liver , Nerve Growth Factors , Reperfusion Injury , Animals , Mice , Alanine Transaminase , Alarmins , Antibodies, Monoclonal/immunology , Aspartate Aminotransferases , Cell Adhesion Molecules, Neuronal/antagonists & inhibitors , Cell Adhesion Molecules, Neuronal/deficiency , Cell Adhesion Molecules, Neuronal/immunology , Cell Adhesion Molecules, Neuronal/ultrastructure , Cell Death , Cell Membrane/pathology , Cell Membrane/ultrastructure , Concanavalin A , Galactosamine , Hepatocytes/pathology , Hepatocytes/ultrastructure , Inflammation/pathology , Lactate Dehydrogenases , Liver/pathology , Microscopy, Electron , Nerve Growth Factors/antagonists & inhibitors , Nerve Growth Factors/deficiency , Nerve Growth Factors/immunology , Nerve Growth Factors/ultrastructure , Neutrophil Infiltration , Reperfusion Injury/pathologyABSTRACT
The RAS-RAF pathway is one of the most commonly dysregulated in human cancers1-3. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation4 of the kinase RAF remains limited. Recent structures of inactive RAF monomer5 and active RAF dimer5-8 bound to 14-3-39,10 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF11 to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS11-13, but the structure of SHOC2 and the architecture of the presumptive SHOC2-PP1C-RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2-PP1C-MRAS complex to an overall resolution of 3 Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.
Subject(s)
Intracellular Signaling Peptides and Proteins , Protein Phosphatase 1 , Signal Transduction , ras Proteins , Cryoelectron Microscopy , Guanosine Triphosphate/metabolism , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Multiprotein Complexes/chemistry , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Multiprotein Complexes/ultrastructure , Mutation , Phosphoserine , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Isoforms/ultrastructure , Protein Phosphatase 1/chemistry , Protein Phosphatase 1/genetics , Protein Phosphatase 1/metabolism , Protein Phosphatase 1/ultrastructure , Substrate Specificity , raf Kinases/metabolism , ras Proteins/chemistry , ras Proteins/genetics , ras Proteins/metabolism , ras Proteins/ultrastructureABSTRACT
Photosynthetic control (PCON) is a protective mechanism that prevents light-induced damage to photosystem I (PSI) by ensuring the rate of NADPH and ATP production via linear electron transfer (LET) is balanced by their consumption in the CO2 fixation reactions. Protection of PSI is a priority for plants since they lack a dedicated rapid-repair cycle for this complex, meaning that any damage leads to prolonged photoinhibition and decreased growth. The imbalance between LET and the CO2 fixation reactions is sensed at the level of the transthylakoid ΔpH, which increases when light is in excess. The canonical mechanism of PCON involves feedback control by ΔpH on the plastoquinol oxidation step of LET at cytochrome b6f. PCON thereby maintains the PSI special pair chlorophylls (P700) in an oxidized state, that allows excess electrons unused in the CO2 fixation reactions to be safely quenched via charge recombination. In this review we focus on angiosperms, considering how photo-oxidative damage to PSI comes about, explore the consequences of PSI photoinhibition on photosynthesis and growth, discuss recent progress in understanding PCON regulation, and finally consider the prospects for its future manipulation in crop plants to improve photosynthetic efficiency.
ABSTRACT
Fragile X syndrome (FXS), the leading monogenic cause of intellectual disability and autism, results from loss of function of the RNA-binding protein FMRP. Here, we show that FMRP regulates translation of neuronal nitric oxide synthase 1 (NOS1) in the developing human neocortex. Whereas NOS1 mRNA is widely expressed, NOS1 protein is transiently coexpressed with FMRP during early synaptogenesis in layer- and region-specific pyramidal neurons. These include midfetal layer 5 subcortically projecting neurons arranged into alternating columns in the prospective Broca's area and orofacial motor cortex. Human NOS1 translation is activated by FMRP via interactions with coding region binding motifs absent from mouse Nos1 mRNA, which is expressed in mouse pyramidal neurons, but not efficiently translated. Correspondingly, neocortical NOS1 protein levels are severely reduced in developing human FXS cases, but not FMRP-deficient mice. Thus, alterations in FMRP posttranscriptional regulation of NOS1 in developing neocortical circuits may contribute to cognitive dysfunction in FXS.
Subject(s)
Cerebral Cortex/embryology , Fragile X Mental Retardation Protein/metabolism , Fragile X Syndrome/embryology , Nitric Oxide Synthase Type I/metabolism , Animals , Cerebral Cortex/metabolism , Fragile X Mental Retardation Protein/genetics , Fragile X Syndrome/metabolism , Fragile X Syndrome/physiopathology , Gene Expression Regulation , Humans , Mice , Mice, Knockout , Neurogenesis , Pyramidal Cells/metabolism , RNA Processing, Post-Transcriptional , Species SpecificityABSTRACT
Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3-5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9-12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.
Subject(s)
Drug Design , Protein Engineering , Proteins/chemical synthesis , Proteins/metabolism , 3T3 Cells , Animals , Cell Biology , Cell Survival , Computational Biology , Endocytosis , Escherichia coli/genetics , Escherichia coli/metabolism , In Vitro Techniques , Kinetics , Ligands , Mice , Microscopy, Atomic Force , Models, Molecular , Synthetic BiologyABSTRACT
Animal embryos are provided by their mothers with a diverse nutrient supply that is crucial for development. In Drosophila, the three most abundant nutrients (triglycerides, proteins and glycogen) are sequestered in distinct storage structures: lipid droplets (LDs), yolk vesicles (YVs) and glycogen granules (GGs). Using transmission electron microscopy as well as live and fixed sample fluorescence imaging, we find that all three storage structures are dispersed throughout the egg but are then spatially allocated to distinct tissues by gastrulation: LDs largely to the peripheral epithelium, YVs and GGs to the central yolk cell. To confound the embryo's ability to sort its nutrients, we employ Jabba and mauve mutants to generate LD-GG and LD-YV compound structures. In these mutants, LDs are mis-sorted to the yolk cell and their turnover is delayed. Our observations demonstrate dramatic spatial nutrient sorting in early embryos and provide the first evidence for its functional importance.
Subject(s)
Drosophila Proteins , Drosophila , Animals , Drosophila/metabolism , Drosophila Proteins/metabolism , Protein Transport , Nutrients , Lipid Droplets/metabolism , Glycogen/metabolism , Lipid Metabolism , Carrier Proteins/metabolismABSTRACT
Lipid droplets (LDs), crucial regulators of lipid metabolism, accumulate during oocyte development. However, their roles in fertility remain largely unknown. During Drosophila oogenesis, LD accumulation coincides with the actin remodeling necessary for follicle development. Loss of the LD-associated Adipose Triglyceride Lipase (ATGL) disrupts both actin bundle formation and cortical actin integrity, an unusual phenotype also seen when the prostaglandin (PG) synthase Pxt is missing. Dominant genetic interactions and PG treatment of follicles indicate that ATGL acts upstream of Pxt to regulate actin remodeling. Our data suggest that ATGL releases arachidonic acid (AA) from LDs to serve as the substrate for PG synthesis. Lipidomic analysis detects AA-containing triglycerides in ovaries, and these are increased when ATGL is lost. High levels of exogenous AA block follicle development; this is enhanced by impairing LD formation and suppressed by reducing ATGL. Together, these data support the model that AA stored in LD triglycerides is released by ATGL to drive the production of PGs, which promote the actin remodeling necessary for follicle development. We speculate that this pathway is conserved across organisms to regulate oocyte development and promote fertility.
Subject(s)
Drosophila Proteins , Prostaglandins , Animals , Lipid Droplets , Actins , Adipogenesis , Drosophila , Lipase , Peroxidases , Drosophila Proteins/geneticsABSTRACT
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
Subject(s)
Chlorophyll , Chlorophyll/chemistry , Chlorophyll/metabolism , Crystallography, X-Ray , Models, Molecular , Photosynthesis , Energy Transfer , Cryoelectron Microscopy , Protein Conformation , Light-Harvesting Protein Complexes/chemistry , Light-Harvesting Protein Complexes/metabolismABSTRACT
Transmembrane channels and pores have key roles in fundamental biological processes1 and in biotechnological applications such as DNA nanopore sequencing2-4, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels5,6, and there have been recent advances in de novo membrane protein design7,8 and in redesigning naturally occurring channel-containing proteins9,10. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge11,12. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore-but not the 12-helix pore-enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.
Subject(s)
Computer Simulation , Genes, Synthetic/genetics , Ion Channels/chemistry , Ion Channels/genetics , Models, Molecular , Synthetic Biology , Cell Line , Cryoelectron Microscopy , Crystallography, X-Ray , Electric Conductivity , Escherichia coli/genetics , Escherichia coli/metabolism , Hydrazines , Ion Channels/metabolism , Ion Transport , Liposomes/metabolism , Patch-Clamp Techniques , Porins/chemistry , Porins/genetics , Porins/metabolism , Protein Engineering , Protein Structure, Secondary , Solubility , Water/chemistryABSTRACT
The yeast INO80 chromatin remodeling complex plays essential roles in regulating DNA damage repair, replication, and promoter architecture. INO80's role in these processes is likely related to its ability to slide nucleosomes, but the underlying mechanism is poorly understood. Here we use ensemble and single-molecule enzymology to study INO80-catalyzed nucleosome sliding. We find that the rate of nucleosome sliding by INO80 increases â¼100-fold when the flanking DNA length is increased from 40 to 60 bp. Furthermore, once sliding is initiated, INO80 moves the nucleosome rapidly at least 20 bp without pausing to re-assess flanking DNA length, and it can change the direction of nucleosome sliding without dissociation. Finally, we show that the Nhp10 module of INO80 plays an auto-inhibitory role, tuning INO80's switch-like response to flanking DNA. Our results indicate that INO80 is a highly processive remodeling motor that is tightly regulated by both substrate cues and non-catalytic subunits.
Subject(s)
Chromatin Assembly and Disassembly , DNA Replication , DNA, Fungal/metabolism , Nucleosomes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , DNA Repair , DNA, Fungal/genetics , High Mobility Group Proteins/genetics , High Mobility Group Proteins/metabolism , Histones/genetics , Histones/metabolism , Nucleosomes/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae Proteins/geneticsABSTRACT
Cytochrome bc1 complexes are ubiquinol:cytochrome c oxidoreductases, and as such, they are centrally important components of respiratory and photosynthetic electron transfer chains in many species of bacteria and in mitochondria. The minimal complex has three catalytic components, which are cytochrome b, cytochrome c1, and the Rieske iron-sulfur subunit, but the function of mitochondrial cytochrome bc1 complexes is modified by up to eight supernumerary subunits. The cytochrome bc1 complex from the purple phototrophic bacterium Rhodobacter sphaeroides has a single supernumerary subunit called subunit IV, which is absent from current structures of the complex. In this work we use the styrene-maleic acid copolymer to purify the R. sphaeroides cytochrome bc1 complex in native lipid nanodiscs, which retains the labile subunit IV, annular lipids, and natively bound quinones. The catalytic activity of the four-subunit cytochrome bc1 complex is threefold higher than that of the complex lacking subunit IV. To understand the role of subunit IV, we determined the structure of the four-subunit complex at 2.9 Å using single particle cryogenic electron microscopy. The structure shows the position of the transmembrane domain of subunit IV, which lies across the transmembrane helices of the Rieske and cytochrome c1 subunits. We observe a quinone at the Qo quinone-binding site and show that occupancy of this site is linked to conformational changes in the Rieske head domain during catalysis. Twelve lipids were structurally resolved, making contacts with the Rieske and cytochrome b subunits, with some spanning both of the two monomers that make up the dimeric complex.
Subject(s)
Rhodobacter sphaeroides , Rhodobacter sphaeroides/chemistry , Cytochromes c , Cytochromes b , Styrene , Cryoelectron Microscopy , Quinones , Lipids , Electron Transport Complex III , Oxidation-ReductionABSTRACT
Active chlorine in the atmosphere is poorly constrained and so is its role in the oxidation of the potent greenhouse gas methane, causing uncertainty in global methane budgets. We propose a photocatalytic mechanism for chlorine atom production that occurs when Sahara dust mixes with sea spray aerosol. The mechanism is validated by implementation in a global atmospheric model and thereby explaining the episodic, seasonal, and location-dependent 13C depletion in CO in air samples from Barbados [J.E. Mak, G. Kra, T. Sandomenico, P. Bergamaschi, J. Geophys. Res. Atmos. 108 (2003)], which remained unexplained for decades. The production of Cl can also explain the anomaly in the CO:ethane ratio found at Cape Verde [K. A. Read et al., J. Geophys. Res. Atmos. 114 (2009)], in addition to explaining the observation of elevated HOCl [M. J. Lawler et al., Atmos. Chem. Phys. 11, 7617-7628 (2011)]. Our model finds that 3.8 Tg(Cl) y-1 is produced over the North Atlantic, making it the dominant source of chlorine in the region; globally, chlorine production increases by 41%. The shift in the methane sink budget due to the increased role of Cl means that isotope-constrained top-down models fail to allocate 12 Tg y-1 (2% of total methane emissions) to 13C-depleted biological sources such as agriculture and wetlands. Since 2014, an increase in North African dust emissions has increased the 13C isotope of atmospheric CH4, thereby partially masking a much greater decline in this isotope, which has implications for the interpretation of the drivers behind the recent increase of methane in the atmosphere.
ABSTRACT
BACKGROUND: Adult mammalian cardiomyocytes have limited proliferative capacity, but in specifically induced contexts they traverse through cell-cycle reentry, offering the potential for heart regeneration. Endogenous cardiomyocyte proliferation is preceded by cardiomyocyte dedifferentiation (CMDD), wherein adult cardiomyocytes revert to a less matured state that is distinct from the classical myocardial fetal stress gene response associated with heart failure. However, very little is known about CMDD as a defined cardiomyocyte cell state in transition. METHODS: Here, we leveraged 2 models of in vitro cultured adult mouse cardiomyocytes and in vivo adeno-associated virus serotype 9 cardiomyocyte-targeted delivery of reprogramming factors (Oct4, Sox2, Klf4, and Myc) in adult mice to study CMDD. We profiled their transcriptomes using RNA sequencing, in combination with multiple published data sets, with the aim of identifying a common denominator for tracking CMDD. RESULTS: RNA sequencing and integrated analysis identified Asparagine Synthetase (Asns) as a unique molecular marker gene well correlated with CMDD, required for increased asparagine and also for distinct fluxes in other amino acids. Although Asns overexpression in Oct4, Sox2, Klf4, and Myc cardiomyocytes augmented hallmarks of CMDD, Asns deficiency led to defective regeneration in the neonatal mouse myocardial infarction model, increased cell death of cultured adult cardiomyocytes, and reduced cell cycle in Oct4, Sox2, Klf4, and Myc cardiomyocytes, at least in part through disrupting the mammalian target of rapamycin complex 1 pathway. CONCLUSIONS: We discovered a novel gene Asns as both a molecular marker and an essential mediator, marking a distinct threshold that appears in common for at least 4 models of CMDD, and revealing an Asns/mammalian target of rapamycin complex 1 axis dependency for dedifferentiating cardiomyocytes. Further study will be needed to extrapolate and assess its relevance to other cell state transitions as well as in heart regeneration.
Subject(s)
Aspartate-Ammonia Ligase , Cell Dedifferentiation , Kruppel-Like Factor 4 , Myocytes, Cardiac , Animals , Mice , Aspartate-Ammonia Ligase/genetics , Aspartate-Ammonia Ligase/metabolism , Cells, Cultured , Myocytes, Cardiac/metabolism , Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/genetics , Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/metabolismABSTRACT
BACKGROUND: New treatments are needed to reduce the risk of progression of coronavirus disease 2019 (Covid-19). Molnupiravir is an oral, small-molecule antiviral prodrug that is active against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We conducted a phase 3, double-blind, randomized, placebo-controlled trial to evaluate the efficacy and safety of treatment with molnupiravir started within 5 days after the onset of signs or symptoms in nonhospitalized, unvaccinated adults with mild-to-moderate, laboratory-confirmed Covid-19 and at least one risk factor for severe Covid-19 illness. Participants in the trial were randomly assigned to receive 800 mg of molnupiravir or placebo twice daily for 5 days. The primary efficacy end point was the incidence hospitalization or death at day 29; the incidence of adverse events was the primary safety end point. A planned interim analysis was performed when 50% of 1550 participants (target enrollment) had been followed through day 29. RESULTS: A total of 1433 participants underwent randomization; 716 were assigned to receive molnupiravir and 717 to receive placebo. With the exception of an imbalance in sex, baseline characteristics were similar in the two groups. The superiority of molnupiravir was demonstrated at the interim analysis; the risk of hospitalization for any cause or death through day 29 was lower with molnupiravir (28 of 385 participants [7.3%]) than with placebo (53 of 377 [14.1%]) (difference, -6.8 percentage points; 95% confidence interval [CI], -11.3 to -2.4; P = 0.001). In the analysis of all participants who had undergone randomization, the percentage of participants who were hospitalized or died through day 29 was lower in the molnupiravir group than in the placebo group (6.8% [48 of 709] vs. 9.7% [68 of 699]; difference, -3.0 percentage points; 95% CI, -5.9 to -0.1). Results of subgroup analyses were largely consistent with these overall results; in some subgroups, such as patients with evidence of previous SARS-CoV-2 infection, those with low baseline viral load, and those with diabetes, the point estimate for the difference favored placebo. One death was reported in the molnupiravir group and 9 were reported in the placebo group through day 29. Adverse events were reported in 216 of 710 participants (30.4%) in the molnupiravir group and 231 of 701 (33.0%) in the placebo group. CONCLUSIONS: Early treatment with molnupiravir reduced the risk of hospitalization or death in at-risk, unvaccinated adults with Covid-19. (Funded by Merck Sharp and Dohme; MOVe-OUT ClinicalTrials.gov number, NCT04575597.).