bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perilipin 3 promotes the formation of membrane domains enriched in diacylglycerol and lipid droplet biogenesis proteins
Authors: Khaddaj Rasha , Schneiter Roger 
Published: September 2022

AbstractLipid droplets (LDs) serve as intracellular stores of energy-rich neutral lipids. LDs form at discrete sites in the endoplasmic reticulum (ER) and they remain closely associated with the ER during lipogenic growth and lipolytic consumption. Their hydrophobic neutral lipid core is covered by a monolayer of phospholipids, which harbors a specific set of proteins. This LD surface is coated and stabilized by perilipins, a family of soluble proteins that specifically target LDs from the cytosol. We have previously used chimeric fusion proteins between perilipins and integral ER membrane proteins to test whether proteins that are anchored to the ER bilayer could be dragged onto the LD monolayer. Expression of these chimeric proteins induces repositioning of the ER membrane around LDs. Here, we test the properties of membrane-anchored perilipins in cells that lack LDs. Unexpectedly, membrane-anchored perilipins induce the formation of crescent-shaped ER membrane domains that have LD-like properties. They are stained by lipophilic dyes and harbor LD marker proteins. In addition, these ER domains are enriched in diacylglycerol (DAG) and in ER proteins that are important for early steps of LD biogenesis, including seipin and Pex30. These ER membrane domains dissolve upon induction of neutral lipid synthesis and the formation of nascent LDs. Formation of these membrane domains in vivo requires DAG, and we show that perilipin 3 (PLIN3) binds to liposomes containing DAG in vitro. Taken together, these observations indicate that perilipin not only serve to stabilize the surface of mature LDs but that they are likely to exert a more active role in early steps of LD biogenesis at ER subdomains enriched in DAG, seipin, and neutral lipid biosynthetic enzymes.
A Second Role for the Second Messenger Cyclic-di-GMP inE. coli: Arresting Cell Growth by Altering Metabolic Flow
Authors: Hwang YuneSahng , Harshey Rasika M. 
Published: September 2022

AbstractC-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. InE. coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN inE. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow.SignificanceThe c-di-GMP signaling network in bacteria not only controls a variety of cellular processes such as motility, biofilms, cell development and virulence, but does so by a dizzying array of mechanisms. The DGC YfiN singularly represents the versatility of this network in that it not only inhibits motility and promotes biofilms, but also arrests growth inE. coliby relocating to the mid-cell and blocking cell division. The work described here reveals that YfiN arrests growth by yet another mechanism inE. coli– changing metabolic flow. This function of YfiN, or of DGCs without autoinhibitory I-sites, may contribute to antibiotic tolerant persisters in relevant niches such as the gut where gluconeogenic sugars are found.
INTERACTION OF THE PERIPLASMIC CHAPERONE SURA WITH THE INNER MEMBRANE PROTEIN SECRETION (SEC) MACHINERY
Authors: Troman Lucy , Alvira Sara , Daum Bertram , Gold Vicki A. M. , Collinson Ian 
Published: September 2022

ABSTRACTGram-negative bacteria are surrounded by two protein-rich membranes with a peptidoglycan layer sandwiched between them. Together they form the envelope (or cell wall), crucial for energy production, lipid biosynthesis, structural integrity, and for protection against the physical and chemical environmental challenges. To achieve envelope biogenesis, periplasmic and outer-membrane proteins (OMPs) must be transported from the cytosol and through the inner-membrane, via the ubiquitous SecYEG protein-channel. Emergent proteins either fold in the periplasm or cross the peptidoglycan (PG) layer towards the outer-membrane for insertion through the β-barrel assembly machinery (BAM). Trafficking of hydrophobic proteins through the periplasm is particularly treacherous given the high protein density and the absence of energy (ATP or chemiosmotic potential). Numerous molecular chaperones assist in the prevention and recovery from aggregation, and of these SurA is known to interact with BAM, facilitating delivery to the outer-membrane. However, it is unclear how proteins emerging from the Sec-machinery are received and protected from aggregation and proteolysis prior to an interaction with SurA. Through biochemical analysis and electron microscopy we demonstrate the binding capabilities of the unoccupied and substrate-engaged SurA to the inner-membrane translocation machinery complex of SecYEG-SecDF-YidC – aka the holo-translocon (HTL). Supported by AlphaFold predictions, we suggest a role for periplasmic domains of SecDF in chaperone recruitment to the protein translocation exit site in SecYEG. We propose that this immediate interaction with a recruited chaperone helps to prevent aggregation and degradation of nascent envelope proteins, facilitating their safe passage to the periplasm and outer-membrane.
Identification and characterization of thousands of bacteriophage satellites across bacteria
Authors: de Sousa Jorge A. Moura , Fillol-Salom Alfred , Penadés José R. , Rocha Eduardo P.C. 
Published: September 2022

AbstractBacteriophage-bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacterial cells. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown for lack of a tool to identify them. We developed a flexible and updateable program to identify satellites in bacterial genomes – SatelliteFinder – and use it to identify the best described families: P4-like, phage inducible chromosomal islands (PICI), capsid-forming PICI, and phage-inducible chromosomal island-like elements (PLE). We vastly expanded the number of described elements to ∼5000, finding hundreds of bacterial genomes with two different families of satellites, and dozens of Escherichia coli genomes with three. Most satellites were found in Proteobacteria and Firmicutes, but some are in novel taxa such as Actinobacteria. We characterized the gene repertoires of satellites, which are variable in size and composition, and their genomic organization, which is very conserved. With the partial exception of PICI and cfPICI, there are few homologous core genes between families of satellites, and even fewer homologous to phages. Hence, phage satellites are ancient, diverse, and probably evolved multiple times independently. Occasionally, core genes of a given family of satellites are found in another, suggesting gene flow between different satellites. Given the many elements found in spite of our conservative approach, the many bacteria infected by phages that still lack known satellites, and the recent proposals for novel families, we speculate that we are at the beginning of the discovery of massive numbers and types of satellites. SatelliteFinder is accessible for the community as a Galaxy service at https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/fmareuil/satellitefinder/SatelliteFinder/0.9
Mapping the cellular and molecular organization of mouse cerebral aging by single-cell transcriptome imaging
Authors: Allen William E. , Blosser Timothy R. , Sullivan Zuri A. , Dulac Catherine , Zhuang Xiaowei 
Published: September 2022

SummaryThe cellular diversity and complex organization of the brain have hindered systematic characterization of age-related changes in its cellular and molecular architecture, limiting our ability to understand the mechanisms underlying its functional decline during aging. Here we generated a high-resolution cell atlas of brain aging within the frontal cortex and striatum using spatially resolved single-cell transcriptomics and quantified the changes in gene expression and spatial organization of major cell types in these brain regions over the lifespan of mice. We observed substantially more pronounced changes in the composition, gene expression and spatial organization of non-neuronal cells over neurons. Our data revealed molecular and spatial signatures of glial and immune cell activation during aging, particularly enriched in subcortical white matter, and identified both similarities and notable differences in cell activation patterns induced by aging and systemic inflammatory challenge. These results provide critical insights into age-related decline and inflammation in the brain.
Mycobacterium tuberculosis DprE1 inhibitor OPC-167832 is active against Mycobacterium abscessus in vitro
Authors: Sarathy Jickky Palmae , Zimmerman Matthew D. , Gengenbacher Martin , Dartois Véronique , Dick Thomas 
Published: September 2022

ABSTRACTThe anti-tuberculosis candidate OPC-167832, an inhibitor of DprE1, was active against Mycobacterium abscessus. Resistance mapped to M. abscessus dprE1, suggesting target retention. OPC-167832 was bactericidal and did not antagonize activity of clinical anti-M. abscessus antibiotics. Due to its moderate potency compared to Mycobacterium tuberculosis, the compound lacked efficacy in a mouse model and is thus not a repurposing candidate. These results identify OPC-167832 – DprE1 as a lead-target couple for a M. abscessus-specific optimization program.
Comparison of gamma-aminobutyric acid, glutamate, and N-acetylaspartate concentrations in the insular cortex between patients with fibromyalgia, rheumatoid arthritis, and healthy controls - a magnetic resonance spectroscopy study
Authors: Aster Hans-Christoph , Hahn Viola , Schmalzing Marc , Homola György A. , Kampf Thomas , Pham Mirko , Üçeyler Nurcan , Sommer Claudia 
Published: September 2022

AbstractFibromyalgia syndrome (FMS) is a chronic pain disorder with hypersensitivity to painful stimuli. A subgroup of patients shows damage to small peripheral nerve fibers. Previous studies support the hypothesis that increased activation of the pain-processing insular cortex is mediated by an imbalance of insular glutamate and γ-aminobutyric acid (GABA) concentrations. Here, we aimed to test this hypothesis in a large cohort of FMS patients comparing data of patients and healthy controls. In addition, we tested the hypothesis whether a reduction in small peripheral nerve fibers relates to glutamate concentrations in the insular cortex. We recruited 102 subjects (all female, 44 FMS patients, 40 healthy age-matched controls, and 19 patients with rheumatoid arthritis (RA) as disease controls. Study participants underwent single-voxel magnetic resonance spectroscopy of the right and left insular cortex. All patients completed questionnaires on symptom severity (pain intensity, impairment due to symptoms, depression). FMS patients were further stratified into subgroups with and without reduced intraepidermal nerve fiber density (IENFD) assessed on skin punch biopsies. We found no intergroup difference of the glutamate/GABA metabolite concentrations between FMS and RA patients and healthy controls. Glutamate/GABA levels did not correlate with symptom severity. Cerebral glutamate concentrations were independent of skin innervation. We found similar insular glutamate/GABA concentrations in FMS patients and disease and healthy controls. Therefore, our data cannot support the hypothesis that a glutamate/GABA mismatch leads to a sensitization of the insular cortex of fibromyalgia patients and thereby induces the symptoms.
Novel Multi-Epitope Vaccine candidate derived from critically important proteins of Monkeypox isolates
Authors: Srivastava Sukrit , Kolbe Michael 
Published: September 2022

ABSTRACTBackgroundOn May 7, 2022, a case of monkeypox virus (MPXV) has been reported to the WHO. It causes a viral zoonotic disease with characteristics comparable to that of smallpox cases. Monkeypox could be a serious health concern as it is already spreading to multiple countries worldwide. To prevent the monkeypox infection and for its early detection, a potential vaccine and diagnostic candidate is urgently required.MethodIn present study we have used different in silico methods to screen the entire genome with its approximately 191 genes for potential epitopes present in proliferation and virulent proteins of monkeypox virus. All protein sequences were retrieved from different genomic and proteome databases listed in Uniprot or NCBI.ResultsIn the present study we have screened potential epitopes from 11 different proteins of Monkeypox. All the included protein play an important role in pathogenesis and/or proliferation of Monkeypox virus. We have identified in total 984 CTL and 168 HTL epitopes with highest score in our epitope screening. The reported epitopes could be potential candidates for the design of an early detection diagnostic kit specific for the monkeypox virus. Out of these target peptides we have included a total of 39 CTL epitopes and 39 HTL epitopes in design of multi-epitope vaccine candidates. These shortlisted epitopes are highly conserved amongst different strains and origin of monkeypox viruses. The population coverage by joint administration of CTL and HTL MEVs is predicted to be high with the epitopes showing potential to bind upto 24 different CTL and HTL HLA allele molecules. The epitopes used in MEVs are examined to be highly immunogenic, non allergic but antigenic, and non toxic. All the CTL and HTL MEVs designed utilizing the epitopes have physiochemical properties favor its over expression in human cells. The optimized cDNA constructs of CTL and HTL MEVs also favor over expression of MEVs in human cells. Overall, the MEV construct proposed by us are fissile for expression in the lab and for further in vivo studies.ConclusionControl and fight against emerging diseases such as MPXV requires pathogen diagnostic and novel vaccine approaches. We screened for several epitopes and designed a MEV providing a potential solution for both purposes. Our method allows rapid screening and provides a rational strategy for the development of vaccine candidate effective in fighting MPXV and other unexpected upcoming diseases.
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
Authors: Padroni Giacomo , Bikaki Maria , Novakovic Mihajlo , Wolter Antje C. , Rüdisser Simon H. , Gossert Alvar D. , Leitner Alexander , Allain Frederic H.-T 
Published: September 2022

ABSTRACTAbstract FigureThe ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further drug development.
Probing mechanical interaction of immune receptors and cytoskeleton by membrane nanotube extraction
Authors: Manca Fabio , Eich Gautier , N’Dao Omar , Normand Lucie , Sengupta Kheya , Limozin Laurent , Puech Pierre-Henri 
Published: September 2022

AbstractThe role of force application in immune cell recognition is now well established, the force being transmitted between the actin cytoskeleton to the anchoring ligands through receptors such as integrins. In this chain, the mechanics of the cytoskeleton to receptor link, though clearly crucial, remains poorly understood. To probe this link, we combine mechanical extraction of membrane tubes from T cells using optical tweezers, and fitting of the resulting force curves with a viscoelastic model taking into account the cell and relevant molecules. We solicit this link using four different antibodies against various membrane bound receptors: antiCD3 to target the T Cell Receptor (TCR) complex, antiCD45 for the long sugar CD45, and two clones of antiCD11 targeting open or closed conformation of LFA1 integrins. Upon disruption of the cytoskeleton, the stiffness of the link changes for two of the receptors, exposing the existence of a receptor to cytoskeleton link - namely TCR-complex and open LFA1, and does not change for the other two where no such a link was expected. Our integrated approach allows us to probe, for the first time, the mechanics of the intracellular receptor-cytoskeleton link in immune cells.
Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination
Authors: McKie Shannon J. , Nicholson Alex S. , Smith Emily , Fawke Stuart , Caroe Eve , Williamson James C. , Butt Benjamin G. , Kolářová Denisa , Peterka Ondřej , Holčapek Michal , Lehner Paul J. , Graham Stephen C. , Deane Janet E. 
Published: September 2022

ABSTRACTMyelin is a multi-layered membrane that tightly wraps neuronal axons enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma membrane proteins and lipids, and disruption of these contacts causes devastating demyelinating diseases. Using two cell-based models of demyelinating sphingolipidoses, we demonstrate that altered lipid metabolism changes the abundance of specific plasma membrane proteins. These altered membrane proteins have known roles in cell adhesion and signalling, with several implicated in neurological diseases. The cell surface abundance of the adhesion molecule Neurofascin, a protein critical for the maintenance of myelin-axon contacts, changes following disruption to sphingolipid metabolism. This provides a direct molecular link between altered lipid abundance and myelin stability. We show that the Neurofascin isoform NF155, but not NF186, interacts directly and specifically with the sphingolipid sulfatide via multiple binding sites and that this interaction requires the full-length extracellular domain of NF155. We demonstrate that NF155 adopts an S-shaped conformation and preferrentially binds sulfatide-containing membranes incis, with important implications for protein arrangement in the tight axon-myelin space. Our work links glycosphingolipid imbalances to disturbance of membrane protein abundance and demonstrates how this may be driven by direct protein-lipid interactions, providing a mechanistic framework to understand the pathogenesis of galactosphingolipidoses.
Cysteine post-translational modifications regulate protein interactions of caveolin-3
Authors: Ashford Fiona , Brown Elaine , Calagan Sarah , Jayasinghe Izzy , Henderson Colin , Fuller William , Wypijewski Krzysztof 
Published: September 2022

AbstractCaveolae are small flask-shaped invaginations of the surface membrane which are proposed to recruit and co-localise signalling molecules. The distinctive caveolar shape is achieved by the oligomeric structural protein caveolin, of which three isoforms exist. Aside from the finding that caveolin-3 is specifically expressed in muscle, functional differences between the caveolin isoforms have not been rigorously investigated. Caveolin-3 is relatively cysteine-rich compared to caveolins 1 and 2, so we investigated its cysteine post-translational modifications. We find that caveolin-3 is palmitoylated at 6 cysteines and becomes glutathiolated following redox stress. We map the caveolin-3 palmitoylation sites to a cluster of cysteines in its C terminal membrane domain, and the glutathiolation site to an N terminal cysteine close to the region of caveolin-3 proposed to engage in protein interactions. Glutathiolation abolishes caveolin-3 interaction with heterotrimeric G protein alpha subunits. Our results indicate that a caveolin-3 oligomer contains up to 66 palmitates, compared to up to 33 for caveolin-1. The additional palmitoylation sites in caveolin-3 therefore provide a mechanistic basis by which caveolae in smooth and striated muscle can possess unique phospholipid and protein cargoes. These unique adaptations of the muscle-specific caveolin isoform have important implications for caveolar assembly and signalling.
Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans
Authors: von Kügelgen Andriko , van Dorst Sofie , Yamashita Keitaro , Sexton Danielle L. , Tocheva Elitza I. , Murshudov Garib , Alva Vikram , Bharat Tanmay A. M. 
Published: September 2022

AbstractDeinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, partly because of its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decades of research into this cell envelope, atomic structural details of the S-layer have remained obscure. In this study, we report the electron cryomicroscopy structure of the D. radiodurans S-layer, showing how it is formed by the Hexagonally Packed Intermediate-layer (HPI) protein arranged in a planar hexagonal lattice. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, with each monomer extending into the adjoining hexamer, leading to a highly interconnected, stable, sheet-like arrangement. Using electron cryotomography and subtomogram averaging from focused ion beam-milled D. radiodurans cells, we obtained a structure of the cellular S-layer, showing how this HPI S-layer coats native membranes on the surface of cells. Our S-layer structure from the diderm bacterium D. radiodurans shows similarities to immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, highlighting shared traits in cell surface organization across different domains of life, with connotations on the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.