bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation and evolution of the sporulation gene set in diverse members of the Firmicutes
Authors: Galperin Michael Y. , Yutin Natalya , Wolf Yuri I. , Alvarez Roberto Vera , Koonin Eugene V. 
Published: February 2022

ABSTRACTThe current classification of the phylum Firmicutes (new name,Bacillota) features eight distinct classes, six of which include known spore-forming bacteria. InBacillus subtilis, sporulation involves up to 500 genes, many of which do not have orthologs in other bacilli and/or clostridia. Previous studies identified about 60 sporulation genes ofB. subtilisthat were shared by all spore-forming members of the Firmicutes. These genes are referred to as the sporulation core or signature although many of these are found also in genomes of non-spore-formers. Using an expanded set of 180 firmicute genomes from 160 genera, including 76 spore-forming species, we investigated the conservation of the sporulation genes, in particular, seeking to identify lineages that lack some of the genes from the conserved sporulation core. The results of this analysis confirmed that many small acid-soluble spore proteins (SASPs), spore coat proteins, and germination proteins, which were previously characterized in bacilli, are missing in spore-forming members ofClostridiaand other classes of Firmicutes. A particularly dramatic loss of sporulation genes was observed in the spore-forming members of the familiesPlanococcaceaeandErysipelotrichaceae. Fifteen species from diverse lineages were found to carryskin(sigK-interrupting) elements of different sizes that all encoded SpoIVCA-like recombinases but did not share any other genes. Phylogenetic trees built from concatenated alignments of sporulation proteins and ribosomal proteins showed similar topology, indicating an early origin and subsequent vertical inheritance of the sporulation genes.IMPORTANCEMany members of the phylum Firmicutes (Bacillota) are capable of producing endospores, which enhance the survival of important Gram-positive pathogens that cause such diseases as anthrax, botulism, colitis, gas gangrene, and tetanus. We show that the core set of sporulation genes, defined previously through genome comparisons of several bacilli and clostridia, is conserved in a wide variety of spore-formers from several distinct lineages of Firmicutes. We also detect widespread loss of sporulation genes in many organisms, particularly within familiesPlanococcaceaeandErysipelotrichaceae.Members of these families, such asLysinobacillus sphaericusandClostridium innocuum, could be excellent model organisms for studying sporulation mechanisms, such as engulfment, formation of the spore coat, and spore germination.
Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation
Authors: Merour Emeric , Hmidan Hatem , Marie Corentine , Helou Pierre-Henri , Lu Haiyang , Potel Antoine , Hure Jean-Baptiste , Clavairoly Adrien , Shih Yi Ping , Goudarzi Salman , Dussaud Sebastien , Ravassard Philippe , Hafizi Sassan , Lo Su Hao , Hassan Bassem A. , Parras Carlos 
Published: February 2022

ABSTRACTThe differentiation of oligodendroglia from oligodendrocyte precursor cells (OPCs) to complex and extensive myelinating oligodendrocytes (OLs) is a multistep process that involves largescale morphological changes with significant strain on the cytoskeleton. While key chromatin and transcriptional regulators of differentiation have been identified, their target genes responsible for the morphological changes occurring during OL myelination are still largely unknown. Here, we show that the regulator of focal adhesion, Tensin3 (Tns3), is a direct target gene of Olig2, Chd7, and Chd8, transcriptional regulators of OL differentiation. Tns3 is transiently upregulated and localized to cell processes of immature OLs, together with integrin-β1, a key mediator of survival at this transient stage. Constitutive Tns3 loss-of-function leads to reduced viability in mouse and humans, with surviving knockout mice still expressing Tns3 in oligodendroglia. Acute deletion of Tns3 in vivo, either in postnatal neural stem cells (NSCs) or in OPCs, leads to a two-fold reduction in OL numbers. We find that the transient upregulation of Tns3 is required to protect differentiating OPCs and immature OLs from cell death by preventing the upregulation of p53, a key regulator of apoptosis. Altogether, our findings reveal a specific time window during which transcriptional upregulation of Tns3 in immature OLs is required for OL differentiation likely by mediating integrin-β1 survival signaling to the actin cytoskeleton as OL undergo the large morphological changes required for their terminal differentiation.
Adenosine A2A Receptor (A2AR) agonists improve survival in K28-hACE2 mice following SARS CoV-2 infection
Authors: Mann Barbara J. , Chhabra Preeti , Ma Mingyang , Brovero Savannah G. , Jones Marieke K. , Linden Joel , Brayman Kenneth L. 
Published: February 2022

ABSTRACTEffective and available therapies for the treatment of COVID-19 disease are limited. Apadenoson is a highly potent selective anti-inflammatory adenosine A2A receptor (A2AR) agonist and potential treatment option for COVID-19 patients. Apadenoson, when administered after infection with SARS CoV-2, was found to decrease weight loss, improve clinical symptoms, reduce levels of a several proinflammatory cytokines and chemokines in bronchial lavage (BAL) fluid, and promote increased survival in K18hACE2 transgenic mice. Of note, administering apadenoson after, but not prior to Covid-19 infection, caused a rapid decrease in lung viral burden. The work presented provides the foundation for further examination of these drugs as a therapy option for COVID-19.SummaryApadenoson therapy improves COVID-19 outcome
DLK-dependent biphasic reactivation of herpes simplex virus latency established in the absence of antivirals
Authors: Dochnal Sara , Merchant Husain Y. , Schinlever Austin R. , Babnis Aleksandra , Depledge Daniel P. , Wilson Angus C. , Cliffe Anna R. 
Published: February 2022

AbstractUnderstanding the molecular mechanism of herpes simplex virus type 1 (HSV-1) latent infection and reactivation in neurons requires the use of model systems. However, establishing a quiescent infection in cultured neurons is problematic as infectious virus released from any productively infected neuron can superinfect the cultures. Here, we describe a new reporter virus, HSV-1 Stayput-GFP, that is defective for cell-to-cell spread and can be used to model latency and reactivation at the single neuron level. Importantly, quiescent infection of neurons with Stayput-GFP can be established without the use of a viral DNA replication inhibitor. The establishment of a quiescent state requires a longer time frame than previous models of HSV latency using DNA replication inhibitors. This results in a decreased ability of the virus to reactivate, and the use of multiple reactivation triggers is required. Using this system, we demonstrate that an initial Phase I wave of lytic gene expression occurs independently of histone demethylase activity and viral DNA replication but is dependent on the neuronal cell stress protein, DLK. Progression into the later, Phase II wave of reactivation, characterized by detectable late viral protein synthesis and a requirement for histone demethylase activity, is also observed with the Stayput-GFP model system. These data demonstrate that the two waves of viral gene expression following HSV-1 reactivation are independent of secondary infection and occur when latent infections are established in the absence of a viral DNA replication inhibitor.ImportanceHerpes simplex virus-1 (HSV-1) enters a latent infection in neurons and periodically reactivates. Reactivation manifests as a variety of clinical symptoms. Studying latency and reactivationin vitrois invaluable, allowing the molecular mechanisms behind both processes to be targeted by therapeutics that reduce the clinical consequences. Here, we describe a novelin vitromodel system using a cell-to-cell spread defective HSV-1, known as Stayput-GFP, which allows for the study of latency and reactivation at the single neuron level. We anticipate this new model system will be an incredibly valuable tool for studying the establishment and reactivation of HSV-1 latent infectionin vitro. Using this model, we find that initial reactivation events are dependent on cellular stress kinase DLK, but independent of histone demethylase activity and viral DNA replication. Our data therefore demonstrate the essential role of DLK in mediating a wave of lytic gene expression unique to reactivation.
Natural Variation Meets Synthetic Biology: Promiscuous Trichome Expressed Acyltransferases from Nicotiana acuminata
Authors: Schenck Craig A. , Anthony Thilani M. , Jacobs MacKenzie , Jones A. Daniel , Last Robert L. 
Published: February 2022

ABSTRACTAcylsugars are defensive, trichome-synthesized sugar esters produced in plants across the Solanaceae (nightshade) family. Although assembled from simple metabolites and synthesized by a relatively short core biosynthetic pathway, tremendous within- and across-species acylsugar structural variation is documented across the family. To advance our understanding of the diversity and the synthesis of acylsugars within the Nicotiana genus, trichome extracts were profiled across the genus coupled with transcriptomics-guided enzyme discovery and in vivo and in vitro analysis. Differences in the types of sugar cores, numbers of acylations, and acyl chain structures contributed to over 300 unique annotated acylsugars throughout Nicotiana. Placement of acyl chain length into a phylogenetic context revealed that an unsaturated acyl chain type was detected in a few closely-related species. A comparative transcriptomics approach identified trichome-enriched Nicotiana acuminata acylsugar biosynthetic candidate enzymes. > 25 acylsugar variants could be produced in a single enzyme assay with four acylsugar acyltransferases (NacASAT1-4) together with structurally diverse acyl-CoAs and sucrose. Liquid chromatography coupled with mass spectrometry screening of in vitro products revealed the ability of these enzymes to make acylsugars not present in Nicotiana plant extracts. In vitro acylsugar production also provided insights into acyltransferase acyl donor promiscuity and acyl acceptor specificity as well as regiospecificity of some ASATs. This study suggests that promiscuous Nicotiana acyltransferases can be used as synthetic biology tools to produce novel and potentially useful metabolites.ONE SENTENCE SUMMARYAnalysis of Nicotiana glandular trichome metabolites and BAHD acyltransferases revealed diverse sucrose and glucose based acylesters.
Global distribution and diversity of prevalent sewage water plasmidomes
Authors: Teudt Frederik , Otani Saria , Aarestrup Frank M. 
Published: February 2022

AbstractSewage water from around the world contains an abundance of short plasmids, a number of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions is only starting to be unveiled. Here, we utilized a previously created dataset of 159,332 assumed small plasmids from 24 different globally collected sewage samples. We investigated the detailed phylogeny as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera to help understand the global sewage plasmidome dynamics.A total of 58,429 circular elements carried genes encoding for plasmid-related features, and MASH distance analyses showed a very high degree of diversity. A single very diverse cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water.Based on functional domain network analysis, we identified three groups of plasmids, mainly replication and mobilization domains. However, these backbone domains were not exclusive to any given group. Acinetobacter was the dominant host genus among theta-replicating plasmids at these size ranges. They contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common resistance genes in sewage plasmidomes and found in the largest number of unique plasmids.While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotics resistance for these pathogens from around the globe.ImportanceAntimicrobial resistance is a global threat to human health inhibiting our ability to treat infectious diseases. This study utilizes sewage water plasmidomes to identify plasmid-derived features, and highlights antimicrobial resistance genes, particularly macrolide resistance to be abundant in sewage water plasmidomes in Firmicutes and Acinetobacter hosts. The emergence of macrolide resistance in these bacteria hints that macrolide selective pressure exists in sewage water, and that the resident bacteria readily can acquire macrolide resistance via small plasmids.
Molecular modeling predicts novel antibody escape mutations in respiratory syncytial virus fusion glycoprotein
Authors: Beach Sierra S. , Hull McKenna , Ytreberg F. Marty , Patel Jagdish Suresh , Miura Tanya A. 
Published: February 2022

AbstractMonoclonal antibodies are increasingly used for the prevention and/or treatment of viral infections. One caveat of their use is the ability of viruses to evolve resistance to antibody binding and neutralization. Computational strategies to predict which mutations will result in antibody resistance would be invaluable because current methods for identifying potential escape mutations are labor intensive and system-biased. Respiratory syncytial virus is an important pathogen for which monoclonal antibodies against the fusion (F) protein are used to prevent severe disease in high-risk infants. In this study, we used an approach that combines molecular dynamics simulations with FoldX to estimate changes in free energy in F protein folding and binding to the motavizumab antibody upon each possible amino acid change. We systematically selected 8 predicted escape mutations and tested them in an infectious clone. Consistent with our F protein stability predictions, replication-effective viruses were observed for each selected mutation. Six of the eight variants showed increased resistance to neutralization by motavizumab. Flow cytometry was used to validate the estimated (model-predicted) effects on antibody binding to F. Using surface plasmon resonance, we determined that changes in the on-rate of motavizumab binding were responsible for the reduced affinity for two novel escape mutations. Our study empirically validates the accuracy of our molecular modeling approach and emphasizes the role of biophysical protein modeling in predicting viral resistance to antibody-based therapeutics that can be used to monitor the emergence of resistant viruses and to design improved therapeutic antibodies.ImportanceRespiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. As no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus will lead to antibody resistance are greatly needed.
Genomic and phenotypic comparisons reveal distinct variants of Wolbachia strain wAlbB
Authors: Martinez Julien , Ross Perran A. , Gu Xinyue , Ant Thomas H. , Murdochy Shivan M. , Tong Lily , da Silva Filipe Ana , Hoffmann Ary A. , Sinkins Steven P. 
Published: February 2022

AbstractThe intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 49 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbiont’s density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programmes and improve the selection of optimal strains in future field interventions.ImportanceDengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the two years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.
Genomic basis and phenotypic manifestation of (non-)parallel serpentine adaptation inArabidopsis arenosa
Authors: Konečná Veronika , Šustr Marek , Požárová Doubravka , Čertner Martin , Krejčová Anna , Tylová Edita , Kolář Filip 
Published: February 2022

ABSTRACTParallel evolution is common in nature and provides one of the most compelling examples of rapid environmental adaptation. In contrast to the recent burst of studies addressing genomic basis of parallel evolution, integrative studies linking genomic and phenotypic parallelism are scarce. Edaphic islands of toxic serpentine soils provide ideal systems for studying rapid parallel adaptation in plants, imposing strong, spatially replicated selection on recently diverged populations. We leveraged threefold independent serpentine adaptation ofArabidopsis arenosaand combined reciprocal transplants, ion uptake phenotyping, and available genome-wide polymorphisms to test if parallelism is manifested to a similar extent at both genomic and phenotypic levels. We found pervasive phenotypic parallelism in functional traits yet with varying magnitude of fitness differences that was congruent with neutral genetic differentiation between populations. Limited costs of serpentine adaptation suggest absence of soil-driven trade-offs. On the other hand, the genomic parallelism at the gene level was significant, although relatively minor. Therefore, the similarly modified phenotypes e.g., of ion uptake arose possibly by selection on different loci in similar functional pathways. In summary, we bring evidence for the important role of genetic redundancy in rapid adaptation involving traits with polygenic architecture.
The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain
Authors: Brown Janae B. , Lee Mark A. , Smith Aaron T. 
Published: February 2022

AbstractMost pathogenic bacteria require ferrous iron (Fe2+) in order to sustain infection within hosts. The ferrous iron transport (Feo) system is the most highly-conserved prokaryotic transporter of Fe2+, but its mechanism remains to be fully characterized. Most Feo systems are composed of two proteins: FeoA, a soluble SH3-like accessory protein and FeoB, a membrane protein that translocates Fe2+ across a lipid bilayer. Some bacterial feo operons encode FeoC, a third soluble, winged-helix protein that remains enigmatic in function. We previously demonstrated that select FeoC proteins bind O2-sensitive [4Fe-4S] clusters via Cys residues, leading to the proposal that some FeoCs could sense O2 to regulate Fe2+ transport. However, not all FeoCs conserve these Cys residues, and FeoC from the causative agent of cholera (Vibrio cholerae) notably lacks any Cys residues, precluding cluster binding. In this work, we determined the NMR structure of VcFeoC, which is monomeric and conserves the helix-turn-helix domain seen in other FeoCs. In contrast, however, the structure of VcFeoC reveals a truncated winged β-sheet in which the cluster-binding domain is notably absent. To test the interactions of VcFeoC with VcFeoB, we used NMR to demonstrate that these proteins interact in a 1:1 stoichiometry with a Kd of ca. 25 μM. Finally, using homology modeling, we predicted the structure of VcNFeoB and used docking to identify an interaction site with VcFeoC, which is confirmed by NMR spectroscopy. These findings provide the first atomic-level structure of VcFeoC and contribute to a better understanding of its role vis-à-vis FeoB.
Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
Authors: Feng Siqian , Rastogi Chaitanya , Loker Ryan E. , Glassford William J. , Rube H. Tomas , Bussemaker Harmen J. , Mann Richard S. 
Published: February 2022

AbstractIn eukaryotes, members of large transcription factor families often exhibit similar DNA binding properties in vitro, yet initiate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which result from alternative gene regulatory networks specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, which are the precursors to the adult appendages and ventral body regions, show that ∼8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the known Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, we identified the homeodomain protein Distal-less (Dll) as a novel Hox cofactor that enhances Scr binding to a different subset of genomic loci. Reporter genes confirm the in vivo roles of Scr+Dll and suggest that ∼1/3 of paralog-specific Hox binding in enhancers is functional. Together, these findings provide a genome-wide view of how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene networks and suggest the importance of multiple, context-specific cofactors.