bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pithoviruses are invaded by repeats that contribute to their evolution and divergence from cedratviruses
Authors: Rigou Sofia , Schmitt Alain , Alempic Jean-Marie , Lartigue Audrey , Vendloczki Peter , Abergel Chantal , Claverie Jean-Michel , Legendre Matthieu 
Published: March 2023

AbstractPithoviridaeare amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery ofPithovirus sibericum, recovered from a 30,000-y-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here we report the isolation and genome sequencing of twoPithoviridaefrom soil samples, in addition to three other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomics study of thePithoviridaefamily to decipher the organization and evolution of their genomes. Our study reveals a non-uniform genome organization in two main regions: one concentrating core genes, and another gene duplications. We also found thatPithoviridaegenomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events and genomic rearrangements, that contribute to their evolution.
Genomic determinants of soil depth niche partitioning in Gagatemarchaeaceae, a novel family of deeply-rooted Thaumarchaeota
Authors: Sheridan Paul O. , Meng Yiyu , Williams Tom A. , Gubry-Rangin Cécile 
Published: March 2023

AbstractKnowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15cm) and subsoils (30-60 cm), most of them corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c). Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary speciation between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also refuted the previous hypothesis of a Thaumarchaeota thermophilic ancestor. Ultimately, this study provides an attractive model for studying mechanisms driving niche partitioning between spatially related ecosystems.
The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates
Authors: Lees John , Pèrtille Fábio , Løtvedt Pia , Jensen Per , Bosagna Carlos Guerrero 
Published: March 2023

AbstractThe mitochondria are central in the cellular response to changing environmental conditions resulting from disease states, environmental exposures or normal physiological processes. Although the influences of environmental stressors upon the nuclear epigenome are well characterized, the existence and role of the mitochondrial epigenome remains contentious. Here, by quantifying the mitochondrial epigenomic response of pineal gland cells to circadian stress, we confirm the presence of extensive cytosine methylation within the mitochondrial genome. Furthermore, we identify distinct epigenetically plastic regions (mtDMRs) which vary in cytosinic methylation, primarily in a non CpG context, in response to stress and in a sex-specific manner. Motifs enriched in mtDMRs contain recognition sites for nuclear-derived DNA-binding factors (ATF4, HNF4A) important in the cellular metabolic stress response, which we found to be conserved across diverse vertebrate taxa. Together, these findings suggest a new layer of mito-nuclear interaction in which the nuclear metabolic stress response directly alters mitochondrial transcriptional dynamics.
“Disruption of Golgi markers by two RILP-directed shRNAs in neurons: a new role for RILP or a neuron-specific off-target phenotype?”
Authors: Yap Chan Choo , Digilio Laura , McMahon Lloyd , Winckler Bettina 
Published: March 2023

AbstractIn neurons, degradation of dendritic cargos requires RAB7 and dynein-mediated retrograde transport to somatic lysosomes. In order to test if the dynein adaptor RILP (RAB-interacting lysosomal protein) mediated the recruitment of dynein to late endosomes for retrograde transport in dendrites, we obtained several knockdown reagents which had been previously validated in non-neuronal cells. We found that striking endosomal phenotypes elicited by one shRILP plasmid were not reproduced by another one. Furthermore, we discovered a profound depletion of Golgi/TGN markers for both shRILP plasmids. This Golgi disruption was only observed in neurons and could not be rescued by re-expression of RILP. This Golgi phenotype was also not found in neurons treated with siRILP or gRILP/Cas9. Lastly, we tested if a different RAB protein that interacts with RILP, namely the Golgi-associated RAB34, might be responsible for the loss of Golgi markers. Expression of a dominant-negative RAB34 did indeed cause changes in Golgi staining in a small subset of neurons but manifested as fragmentation rather than loss of markers. Unlike in non-neuronal cells, interference with RAB34 did not cause dispersal of lysosomes in neurons. Based on multiple lines of experimentation, we conclude that the neuronal Golgi phenotype observed with shRILP is likely off-target in this cell type specifically. Any observed disruptions of endosomal trafficking caused by shRILP in neurons might thus be downstream of Golgi disruption. Different approaches will be needed to test if RILP is required for late endosomal transport in dendrites. Cell type-specific off-target phenotypes therefore likely occur in neurons, making it prudent to re-validate reagents that were previously validated in other cell types.
Molecular characterization of the N-terminal half of TasA during functional amyloid assembly and its contribution toBacillus subtilisbiofilm formation
Authors: Cámara-Almirón Jesús , Domínguez-García Laura , Mammeri Nadia El , Lends Alons , Habenstein Birgit , Vicente Antonio de , Loquet Antoine , Romero Diego 
Published: March 2023

AbstractBiofilms are bacterial communities that result from a cell differentiation process that leads to the secretion of an extracellular matrix (ECM) by part of the bacterial population. InBacillus subtilis,the main protein component of the ECM is the functional amyloid TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved amongBacillusspecies and contains a protein domain, the amyloid core (AcTasA), which is critical for the formation of the amyloid architecture. In this study, we demonstrate that recombinantly purified AcTasAin vitroretains biochemical properties previously observed for the entire protein. Further analysis of the AcTasA amino acid sequence revealed two amyloidogenic stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these amyloidogenic stretches found in AcTasA revealed their amyloid capacityin vitro, contributing to the amyloid nature of AcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA.In vivoandin vitroexperiments with versions of TasA carrying the substitutions D64A, K68A, and D69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid polymerization. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of functional amyloids.
Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species:Archangium lansiniumsp. nov.,Myxococcus landrumussp. nov.,Nannocystis bainbridgeasp. nov.,Nannocystis poenicansasp. nov.,Nannocystis radixulmasp. nov.,Polyangium mundeleiniumsp. nov.,Pyxidicoccus parkwaysissp. nov.,Sorangium ateriumsp. nov.,Stigmatella ashevillenasp. nov
Authors: Ahearne Andrew , Phillips Kayleigh , Knehans Thomas , Hoing Miranda , Dowd Scot E. , Stevens D. Cole 
Published: March 2023

ABSTRACTNatural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Continued discovery and sequencing of novel myxobacteria from the environment provides BGCs for the genome mining pipeline. Herein, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates where determined to be novel species of myxobacteria including representatives from the generaArchangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, andStigmatella. Growth profiles, biochemical assays, and descriptions are provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Utilizing complete or near complete genome sequences we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
GABAergic synaptic scaling is triggered by changes in spiking activity rather than AMPA receptor activation
Authors: Gonzalez-Islas Carlos , Sabra Zahraa , Fong Ming-fai , Bülow Pernille , Yong Nicholas Au , Engisch Kathrin , Wenner Peter 
Published: March 2023

AbstractHomeostatic plasticity represents a set of mechanisms that are thought to recover some aspect of neural function. One such mechanism called AMPAergic scaling was thought to be a likely candidate to homeostatically control spiking activity. However, recent findings have forced us to reconsider this idea as several studies suggest AMPAergic scaling is not directly triggered by changes in spiking. Moreover, studies examining homeostatic perturbationsin vivohave suggested that GABAergic synapses may be more critical in terms of spiking homeostasis. Here we show results that GABAergic scaling can act to homeostatically control spiking levels. We found that perturbations which increased or decreased spiking in cortical cultures triggered multiplicative GABAergic upscaling and downscaling, respectively. In contrast, we found that changes in AMPAR or GABAR transmission only influence GABAergic scaling through their indirect effect on spiking. We propose that GABAergic scaling represents a stronger candidate for spike rate homeostat than AMPAergic scaling.Significance StatementThe nervous system maintains excitability in order to perform network behaviors when called upon to do so. Networks are thought to maintain spiking levels through homeostatic synaptic scaling, where compensatory multiplicative changes in synaptic strength are observed following alterations in cellular spike rate. Although we demonstrated that AMPAergic synaptic scaling does not appear meet these criteria as a spike rate homeostat, we now show that GABAergic scaling could play this role. Here we present evidence that the characteristics of GABAergic scaling place it in an excellent position to be a spiking homeostat. This work highlights the importance of inhibitory circuitry in the homeostatic control of excitability. Further, it provides a point of focus into neurodevelopmental disorders where excitability is impaired.
RPL26/uL24 UFMylation is essential for ribosome-associated quality control at the endoplasmic reticulum
Authors: Scavone Francesco , Gumbin Samantha C. , DaRosa Paul A. , Kopito Ron R. 
Published: March 2023

AbstractRibosomes that stall while translating cytosolic proteins are incapacitated by incomplete nascent chains, termed “arrest peptides” (APs) that are destroyed by the ubiquitin proteasome system (UPS) via a process known as the ribosome-associated quality control (RQC) pathway. By contrast, APs on ribosomes that stall while translocating secretory proteins into the endoplasmic reticulum (ER-APs) are shielded from cytosol by the ER membrane and the tightly sealed ribosome-translocon junction (RTJ). How this junction is breached to enable access of cytosolic UPS machinery and 26S proteasomes to translocon- and ribosome-obstructing ER-APs is not known. Here, we show that UPS and RQC-dependent degradation of ER-APs strictly requires conjugation of the ubiquitin-like (Ubl) protein UFM1 to 60S ribosomal subunits at the RTJ. Therefore, UFMylation of translocon-bound 60S subunits modulates the RTJ to promote access of proteasomes and RQC machinery to ER-APs.Significance StatementUFM1 is a ubiquitin-like protein that is selectively conjugated to the large (60S) subunit of ribosomes bound to the endoplasmic reticulum (ER), but the specific biological function of this modification is unclear. Here, we show that UFMylation facilitates proteasome-mediated degradation of arrest polypeptides (APs) which are generated following splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. We propose that UFMylation weakens the tightly sealed ribosome-translocon junction, thereby allowing the cytosolic ubiquitin-proteasome and ribosome-associated quality control machineries to access ER-APs.
Generation of a SARS-CoV-2 reverse genetics system and novel human lung cell lines that exhibit high virus-induced cytopathology
Authors: Khan Juveriya Qamar , Rohamare Megha , Rajamanickam Karthic , Bhanumathy Kalpana K , Lew Jocelyne , Kumar Anil , Falzarano Darryl , Vizeacoumar Franco J , Wilson Joyce A 
Published: March 2023

AbstractThe global COVID-19 pandemic continues with an increasing number of cases worldwide and the emergence of new SARS-CoV-2 variants. In our study, we have developed novel tools with applications for screening antivirals, identifying virus-host dependencies, and characterizing viral variants. Using reverse genetics, we rescued SARS-CoV-2 Wuhan1 (D614G variant) wild type (WTFL) and reporter virus (NLucFL) using molecular BAC clones. The replication kinetics, plaque morphology and titers were comparable between rescued molecular clones and a clinical isolate (VIDO-01 strain), thus providing confidence that the rescued viruses can be used as effective replication tools. Furthermore, the reporter SARS-CoV-2 NLucFL virus exhibited robust luciferase values over the time course of infection and was used to develop a rapid antiviral assay using remdesivir as proof-of-principle. In addition, as a tool to study lung-relevant virus-host interactions, we established novel human lung cell lines that support SARS-CoV-2 infection with high virus-induced cytopathology. Six lung cell lines (NCI-H23, A549, NCI-H1703, NCI-H520, NCI-H226, and HCC827) and HEK293T cells, were transduced to stably express ACE2 and tested for their ability to support virus infection. A549ACE2B1 and HEK293TACE2A2 cell lines exhibited more than 70% virus-induced cell death and a novel lung cell line NCI-H23ACE2A3 showed about ∼99% cell death post-infection. These cell lines are ideal for assays relying on live-dead selection and are currently being used in CRISPR knockout and activation screens in our lab.ImportanceWe used a reverse genetics system to generate a wild type as well as a nanoluciferase-expressing reporter clone of SARS-CoV-2. The reporter virus allows for rapid transient replication assays and high throughput screens by detection of virus replication using luciferase assays. In addition, the reverse genetic system can be used to generate mutant viruses to study phenotypes of variant mutations. Additionally, unique human lung cell lines supporting SARS-CoV-2 replication will aid in studying the virus in a lung-relevant environment and based on high cytopathology induced in some cell lines, will be useful for screens that rely on virus-induced cell death for selection. Our study aims to enhance and contribute to the current replication tools available to study SARS-CoV-2 by providing rapid methods, virus clones and novel lung cell lines.
Infections in biological and targeted synthetic drug use in rheumatoid arthritis: where do we stand? A scoping review and meta-analysis
Authors: Bergmans BJM , Gebeyehu BY , van Puijenbroek EP , Van Deun K , Kleinberg B , Murk JL , de Vries E 
Published: March 2023

AbstractObjectivesThe advent of biological and targeted synthetic therapies has revolutionised rheumatoid arthritis (RA) treatment. However, this has come at the price of an increased risk of infections. The aim of this study was to present an integrated overview of both serious and non-serious infections, and to identify potential predictors of infection risk in RA patients using biological or targeted synthetic drugs.DesignWe systematically reviewed available literature from PubMed and Cochrane and performed multivariate meta-analysis with meta-regression on the reported infections. Randomised controlled trials and prospective and retrospective observational studies including patient registry studies were analysed, combined as well as separately. We excluded studies focusing on viral infections only.ResultsInfections were not reported in a standardised manner. Meta-analysis showed significant heterogeneity that persisted after forming subgroups by study design and follow-up duration. Overall, the pooled proportions of patients experiencing an infection during a study were 0.30 (95%CI, 0.28-0.33) and 0.03 (95%CI, 0.028-0.035) for any kind of infections or serious infections only, respectively. We found no potential predictors that were consistent across all study subgroups.ConclusionsThe high heterogeneity and the inconsistency of potential predictors between studies show that we do not yet have a complete picture of infection risk in RA patients using biological or targeted synthetic drugs. Besides, we found non-serious infections outnumbered serious infections by a factor 10:1, but only few studies have focused on their occurrence. Future studies should apply a uniform method of infectious adverse event reporting and also focus on non-serious infections and their impact on treatment decisions and quality of life.
Functional and regulatory diversification ofPeriodgenes responsible for circadian rhythm in vertebrates
Authors: Kwak Jun Soung , León-Tapia M. Ángel , Diblasi Celian , Manousi Domniki , Grønvold Lars , Sandvik Guro Katrine , Saitou Marie 
Published: March 2023

AbstractThe Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular through the transcription-translation feedback loop. While thePeriodgene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification ofPergenes across vertebrates are not well known. In this study, we comprehensively investigated the evolution ofPergenes, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events ofPergenes, though no simple association was observed between ecological factors andPergene numbers in each species. Among salmonid fish species, theper3gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region inPer1andPer3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution ofPergenes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.SignificanceThePeriod(Per) genes play essential roles in the circadian rhythm in animals. In this study, we comprehensively investigated the evolutionary diversification of the three types ofPeriodgenes in vertebrates. As a result, we observed a rapid evolution and sub-functionalization of these genes, especially adaptive diversification signatures in the protein-binding region, which plays a crucial role in regulating circadian rhythms. This underscores the fine-tuned contribution ofPergenes in the biological clock’s precision and adaptability across various vertebrate taxa.
Tetracycline-dependent inhibition of mitoribosome protein elongation in mitochondrial disease mutant cells suppresses IRE1α to promote cell survival
Authors: Ronayne Conor T. , Bennett Christopher F. , Perry Elizabeth A. , Kantorovic Noa , Puigserver Pere 
Published: March 2023

AbstractMitochondrial diseases are a group of disorders defined by defects in oxidative phosphorylation caused by nuclear- or mitochondrial-encoded gene mutations. A main cellular phenotype of mitochondrial disease mutations are redox imbalances and inflammatory signaling underlying pathogenic signatures of these patients. Depending on the type of mitochondrial mutation, certain mechanisms can efficiently rescue cell death vulnerability. One method is the inhibition of mitochondrial translation elongation using tetracyclines, potent suppressors of cell death in mitochondrial disease mutant cells. However, the mechanisms whereby tetracyclines promote cell survival are unknown. Here, we show that in mitochondrial mutant disease cells, tetracycline-mediated inhibition of mitochondrial ribosome (mitoribosome) elongation promotes survival through suppression of the ER stress IRE1α protein. Tetracyclines increased levels of the splitting factor MALSU1 (Mitochondrial Assembly of Ribosomal Large Subunit 1) at the mitochondria with recruitment to the mitoribosome large subunit. MALSU1, but not other quality control factors, was required for tetracycline-induced cell survival in mitochondrial disease mutant cells during glucose starvation. In these cells, nutrient stress induced cell death through IRE1α activation associated with a strong protein loading in the ER lumen. Notably, tetracyclines rescued cell death through suppression of IRE1α oligomerization and activity. Consistent with MALSU1 requirement, MALSU1 deficient mitochondrial mutant cells were sensitive to glucose-deprivation and exhibited increased ER stress and activation of IRE1α that was not reversed by tetracyclines. These studies show that inhibition of mitoribosome elongation signals to the ER to promote survival, establishing a new interorganelle communication between the mitoribosome and ER with implications in basic mechanisms of cell survival and treatment of mitochondrial diseases.