bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population
Authors: Wei Jia , Matthews Philippa C. , Stoesser Nicole , Newton John N , Diamond Ian , Studley Ruth , Taylor Nick , Bell John I , Farrar Jeremy , Kolenchery Jaison , Marsden Brian D. , Hoosdally Sarah , Jones E Yvonne , Stuart David I , Crook Derrick W. , Peto Tim E. A. , Walker A. Sarah , Pouwels Koen B. , Eyre David W. ,   the COVID-19 Infection Survey team
Published: December 2022

AbstractFollowing primary SARS-CoV-2 vaccination, understanding the relative extent of protection against SARS-CoV-2 infection from boosters or from breakthrough infections (i.e. infection in the context of previous vaccination) has important implications for vaccine policy. In this study, we investigated correlates of protection against Omicron BA.4/5 infections and anti-spike IgG antibody trajectories after a third/booster vaccination or breakthrough infection following second vaccination in 154,149 adults ≥18y from the United Kingdom general population. We found that higher anti-spike IgG antibody levels were associated with increased protection against Omicron BA.4/5 infection and that breakthrough infections were associated with higher levels of protection at any given antibody level than booster vaccinations. Breakthrough infections generated similar antibody levels to third/booster vaccinations, and the subsequent declines in antibody levels were similar to or slightly slower than those after third/booster vaccinations. Taken together our findings show that breakthrough infection provides longer lasting protection against further infections than booster vaccinations. For example, considering antibody levels associated with 67% protection against infection, a third/booster vaccination did not provide long-lasting protection, while a Delta/Omicron BA.1 breakthrough infection could provide 5-10 months of protection against Omicron BA.4/5 reinfection. 50-60% of the vaccinated UK population with a breakthrough infection would still be protected by the end of 2022, compared to <15% of the triple-vaccinated UK population without previous infection. Although there are societal impacts and risks to some individuals associated with ongoing transmission, breakthrough infection could be an efficient immune-boosting mechanism for subgroups of the population, including younger healthy adults, who have low risks of adverse consequences from infection.
A Minimal Model of CD95 Signal Initiation Revealed by Advanced Super-resolution and Multiparametric Fluorescence Microscopy
Authors: Bartels Nina , van der Voort Nicolaas T M , Greife Annemarie , Bister Arthur , Wiek Constanze , Seidel Claus A M , Monzel Cornelia 
Published: December 2022

AbstractUnraveling the spatiotemporal organization and dynamical interactions of receptors in the plasma membrane remains a key challenge for our mechanistic understanding of cell signal initiation. A paradigm of such process is the oligomerization of TNF receptor CD95 during apoptosis signaling, where molecular configurations are yet to be defined. Here, we scrutinize proposed oligomerization models in live cells, establishing a molecular sensitive imaging toolkit including time-resolved FRET spectroscopy, quantitative STED microscopy, confocal Photobleaching Step Analysis and FCS. CD95 interactions were probed over molecular concentrations of few to ∼ 1000 molecules/µm2, over ns to hours, and molecular to cellular scales. We further established high-fidelity monomer and dimer controls for quantitative benchmarking. Efficient apoptosis was already observed when ∼ 8 to 17% monomeric CD95 oligomerize to dimers/trimers after ligand binding. Our multiscale study highlights the importance of molecular concentrations, of the native environment, and reveals a minimal oligomerization model of CD95 signal initiation.
Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen
Authors: Yao Ruhui , Hou Jian , Zhang Xin , Li Yi , Lai Junhui , Wu Qinqin , Liu Qinglian , Zhou Lei 
Published: December 2022

ABSTRACTThe SARS-CoV-2 virus has been on a rampage for more than two years. Vaccines in combination with neutralizing antibodies (NAbs) against SARS-CoV-2 carry great hope in the treatment and final elimination of COVID-19. However, the relentless emergence of variants of concern (VOC), including the most recent Omicron variants, presses for novel measures to counter these variants that often show immune evasion. Hereby we developed a targeted photodynamic approach to neutralize SARS-CoV-2 by engineering a genetically encoded photosensitizer (SOPP3) to a diverse list of antibodies targeting the WT spike protein, including human antibodies isolated from a 2003 SARS patient, potent monomeric and multimeric nanobodies targeting RBD, and non-neutralizing antibodies (non-NAbs) targeting the more conserved NTD region. As confirmed by pseudovirus neutralization assay, this targeted photodynamic approach significantly increased the efficacy of these antibodies, especially that of non-NAbs, against not only the WT but also the Delta strain and the heavily immune escape Omicron strain (BA.1). Subsequent measurement of infrared phosphorescence at 1270 nm confirmed the generation of singlet oxygen (1O2) in the photodynamic process. Mass spectroscopy assay uncovered amino acids in the spike protein targeted by1O2. Impressively, Y145 and H146 form an oxidization “hotspot”, which overlaps with the antigenic “supersite” in NTD. Taken together, our study established a targeted photodynamic approach against the SARS-CoV-2 virus and provided mechanistic insights into the photodynamic modification of protein molecules mediated by1O2.
FMRP phosphorylation modulates neuronal translation through YTHDF1
Authors: Zou Zhongyu , Wei Jiangbo , Chen Yantao , Kang Yunhee , Shi Hailing , Yang Fan , Chen Shijie , Zhou Ying , Sepich-Poore Caraline , Zhuang Xiaoxi , Zhou Xiaoming , Jiang Hualiang , Wen Zhexing , Jin Peng , Luo Cheng , He Chuan 
Published: December 2022

AbstractTranslation activation of local synaptic mRNAs is critical to learning and memory1-3. Despite extensive studies on how phosphorylation of ribosomal proteins and translation factors enables timely response to exogenous stimuli4,our knowledge on molecular pathways utilized by RNA binding proteins (RBPs) to control translation of specific mRNAs remains incomplete. We have previously found that YTHDF1 regulates depolarization-induced protein synthesis by promoting translation ofN6-methyladenosine (m6A)-modified transcripts5. Here we report an unexpected mechanism that the stimuli-induced neuronal translation is mediated by phosphorylation of a YTHDF1-binding protein FMRP. Phosphorylation of FMRP serine 499 induced by neuronal depolarization alters the condensing behavior of prion-like protein YTHDF1. Unphosphorylated FMRP sequesters YTHDF1 away from the translation initiation complex, whereas the stimulation-induced FMRP phosphorylation releases YTHDF1 to form translational active condensates with the ribosome to activate translation of YTHDF1 target transcripts. In fragile X syndrome (FXS) models characterized by low FMRP expression, we observed YTHDF1-mediated hyperactive translation, which notably impacts FXS pathophysiology. Developmental defects in an FXS forebrain organoid model could be reversed by a selective small-molecule inhibitor of YTHDF1 which acts by suppressing its condensation in neurons. We characterized transcriptome-wide mRNA translation with inhibitor treatment in organoids and identified targets that explain alleviated FXS pathology. Our study thus reveals FMRP and its phosphorylation as an important regulator of the activity-dependent translation during neuronal development and stimulation, and identifies YTHDF1 as a potential therapeutic target for FXS in which developmental defects caused by FMRP depletion could be reversed through YTHDF1 inhibition.
Transposable elements drive the evolution of metazoan zinc finger genes
Authors: Wells Jonathan N. , Chang Ni-Chen , McCormick John , Coleman Caitlyn , Ramos Nathalie , Jin Bozhou , Feschotte Cédric 
Published: December 2022

AbstractCys2-His2 Zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that the targeting and repression of lineage-specific transposable elements (TEs) plays a major role in the diversification of the Kruppel-associated box ZNF (KZNF) subfamily, which predominates in tetrapod genomes. At present, it is unknown whether this function and co-evolutionary relationship is unique to KZNFs, or a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver in the diversification of ZNFs in animals. Sampling from more than 4000 animal genome assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution, both within and between major taxonomic groups. Using computational predictions, we show that ZNFs preferentially bind TEs in a diverse set of representative animal species. We further investigate one of the most expansive ZNF subfamilies found in cyprinid fish, which are characterized by a conserved domain we dubbed theFishN-terminalZinc-finger associated (FiNZ) domain. FiNZ-ZNFs have dramatically expanded in several fish species, including the zebrafish in which we predict ~700 FiNZ-ZNF genes. Almost all are located on the long arm of chromosome 4, and recent duplicates are evolving adaptively under positive selection. Like mammalian KZNFs, the bulk of zebrafish FiNZ-ZNFs are expressed in waves at the onset of zygotic genome activation. Blocking FiNZ-ZNF translation using morpholinos during early zebrafish embryogenesis results in a global de-repression of young, transcriptionally active TEs, likely driven by the failure to establish heterochromatin over these elements. Together, these data suggest that ZNF diversification has been intimately connected to TE expansion throughout animal evolution and that families of ZNFs have been deployed independently in fish and mammals to repress TEs during early embryogenesis.
Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein
Authors: Marino Nicole D. , Talaie Alexander , Carion Héloïse , Johnson Matthew C. , Zhang Yang , Silas Sukrit , Li Yuping , Bondy-Denomy Joseph 
Published: December 2022

SummaryBacteria have evolved multiple defense systems, including CRISPR-Cas, to cleave the DNA of phage and mobile genetic elements (MGE). In turn, phage have evolved anti-CRISPR (Acr) proteins that use novel and co-opted mechanisms to block DNA binding or cleavage. Here, we report that an anti-CRISPR (AcrVA2) unexpectedly inhibits Cas12a biogenesis by triggering translation-dependent destruction of its mRNA. AcrVA2 specifically clears the mRNA of Cas12a by recognizing and binding its N-terminal polypeptide. Mutating conserved N-terminal amino acids in Cas12a prevents binding and inhibition by AcrVA2 but also decreases Cas12a anti-phage activity. This mechanism therefore enables AcrVA2 to specifically inhibit divergent Cas12a orthologs while constraining its ability to escape inhibition. AcrVA2 homologs are found on diverse MGEs across numerous bacterial classes, typically in the absence of Cas12a, suggesting that this protein family may induce similar molecular outcomes against other targets. These findings reveal a new gene regulatory strategy in bacteria and create opportunities for polypeptide-specific gene regulation in prokaryotes and beyond.
Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic
Authors: Silva Kalinga Pavan T. , Sundar Ganesh , Khare Anupama 
Published: December 2022

AbstractThe rise of antimicrobial resistance has motivated the development of antibiotics that have multiple cellular targets, to theoretically reduce the frequency of resistance evolution, but adaptive trajectories and genetic determinants of resistance against such antibiotics are understudied. Here we investigate these in methicillin resistantStaphylococcus aureus(MRSA) using experimental evolution of ten independent populations in the presence of delafloxacin (DLX), a novel fluoroquinolone that targets both DNA gyrase and topoisomerase IV. We show that coding sequence mutations and genomic amplifications of the gene encoding a poorly characterized efflux pump, SdrM, lead to the evolution of high DLX resistance, circumventing the requirement for mutations in the target enzymes. Almost all of our evolved populations had one of two SdrM coding sequence mutations, which led to moderate DLX resistance. Additionally, these populations had 13 distinct genomic amplifications, each containingsdrMand two adjacent genes encoding efflux pumps, which resulted in up to 100-fold higher DLX resistance. While increasedsdrMexpression provided the selective advantage of the amplification in the DLX evolution, the adjacent efflux pumps hitchhiking in the genomic amplification contributed to cross-resistance against the aminoglycoside streptomycin. Finally, lack ofsdrMnecessitated mutations in both DNA gyrase and topoisomerase IV to evolve DLX resistance, and the presence ofsdrMthus increased the frequency of resistance evolution. Our study highlights that instead of reduced rates of resistance, evolution of resistance to antibiotics with multiple cellular targets can involve alternate high-frequency evolutionary paths such as genomic amplifications of efflux pumps, that may cause unexpected alterations of the fitness landscape, including antibiotic cross-resistance.
A regulatory toolkit of arabinose-inducible artificial transcription factors for Gram-negative bacteria
Authors: Naseri Gita , Raasch Hannah , Charpentier Emmanuelle , Erhardt Marc 
Published: December 2022

AbstractThe Gram-negative bacteriaSalmonellaTyphimurium andEscherichia coliare important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research, biomedicine, and biotechnological applications, we developed a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 andArabidopsis-derivedDNA-binding proteins, allowing to control gene expression inE. coliandSalmonellaover a wide inducer concentration range. As a proof-of-concept, we employed the developed ATFs to engineer aSalmonellabiosensorstrain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which responds to the presence of alkaloid drugs with quantifiable fluorescent output. We demonstrated that SALSOR 0.2 was able to detect the presence of the antitussive noscapine alkaloid with ~2.3-fold increased fluorescent signal over background noise compared to a previously described biosensor. Moreover, we used plant-derived ATFs to control β-carotene biosynthesis inE. coli, which resulted in ~1.6-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter. The arabinose-inducible ATFs reported here thus enhance the synthetic biology repertoire of transcriptional regulatory modules that allow tuning protein expression in the Gram-negative model organismsSalmonellaandE. coli.
Different low-complexity regions of SFPQ play distinct roles in the formation of biomolecular condensates
Authors: Marshall Andrew C. , Cummins Jerry , Kobelke Simon , Zhu Tianyi , Widagdo Jocelyn , Anggono Victor , Hyman Anthony , Fox Archa H. , Bond Charles S. , Lee Mihwa 
Published: December 2022

ABSTRACTDemixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism governing the organisation of molecules within the cell. Long disordered low complexity regions (LCRs) are a common feature of proteins that form biomolecular condensates. RNA-binding proteins with prion-like composition have been highlighted as drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQin vitroand in the cell. In contrast, we find that, unexpectedly, the longer N-terminal prion-like LCR of SFPQ attenuates condensation, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. Our data add nuance to the emerging understanding of biomolecular condensate formation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation.Graphical Abstract
The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence
Authors: Lee UnJin , Arsala Deanna , Xia Shengqian , Li Cong , Ali Mujahid , Svetec Nicolas , Langer Christopher B , Sobreira Débora R. , Eres Ittai , Sosa Dylan , Chen Jianhai , Zhang Li , Reilly Patrick , Guzzetta Alexander , Emerson J.J. , Andolfatto Peter , Zhou Qi , Zhao Li , Long Manyuan 
Published: December 2022

AbstractPrevious evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment of distally duplicated genes (enhancer capture) is an efficient mechanism for modulating tissue-specific production of pre-existing proteins. By leveraging genomic asymmetries in synteny and function that distinguish new genes evolving under enhancer capture-divergence (ECD) from those evolving under previous models, we performed a co-expression analysis onDrosophila melanogastertissue data to show the generality of ECD as a significant evolutionary driver of asymmetric, distally duplicated genes. We use the recently evolved geneHP6/Umbrea, which duplicated <15 million years ago (mya), as an example of the ECD process. By assaying genome-wide chromosomal conformations in multipleDrosophilaspecies, we show thatHP6/Umbreawas inserted into a pre-existing, evolutionarily stable 3D genomic structure spanning over 125kb. We then utilize this data to identify a newly discovered enhancer (FLEE1), buried within the coding region of the highly conserved, essential geneMFS18, that likely neo-functionalizedHP6/Umbrea, thereby driving the new duplicate gene copy to fixation. Finally, we demonstrate ancestral transcriptional co-regulation ofHP6/Umbrea’s future insertion site using single-cell transcriptomics, illustrating how enhancer capture provides a highly evolvable, one-step solution to Ohno’s Dilemma. The intuitive molecular mechanism underpinning the ECD model unveils a novel and robust framework to understand the fixation and neofunctionalization of distally duplicated genes.
Regulation of replicative histone RNA metabolism by the histone chaperone ASF1
Authors: Mendiratta Shweta , Ray-Gallet Dominique , Gatto Alberto , Lemaire Sébastien , Kerlin Maciej A. , Coulon Antoine , Almouzni Geneviève 
Published: December 2022

SUMMARYIn S phase, duplication and assembly of the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored a potential role of histone chaperones in this process thereby linking chromatin assembly with histone production in human cells. Depletion of the ASF1 chaperone specifically decreased the pool of replicative histones both at the levels of soluble protein and total RNA, while depletion of CAF-1 did not. Most replicative histone genes decreased in their overall expression as revealed by total RNA-seq. In contrast, both their newly synthesized RNAs and nascent RNAs at transcription sites increased as shown by 4sU-labeled RNA-seq and single-molecule RNA FISH, respectively. Further inspection of the sequences corresponding to replicative histone RNAs showed a 3’ processing defect, leading to unprocessed transcripts usually targeted for degradation. We discuss how this regulation of replicative histone RNA metabolism by ASF1 fine-tunes the histone dosage to avoid unbalanced situations deleterious for cell survival.
Divergent and diversified proteome content across a serially acquired plastid lineage
Authors: Novák Vanclová Anna M. G. , Nef Charlotte , Vancl Adél , Liu Fuhai , Füssy Zoltán , Bowler Chris , Dorrell Richard G. 
Published: December 2022

AbstractDinoflagellates are a diverse group of ecologically significant micro-eukaryotes, prone to the loss and replacement of their plastids via serial endosymbiosis. One such replacement took place in the ancestors of the Kareniaceae, which harbor haptophyte-derived plastids containing the pigment fucoxanthin, instead of the ancestral peridinin dinoflagellate plastid. The metabolic functions of the fucoxanthin plastid are performed by a diverse range of nucleus-encoded and plastid-targeted proteins, which may originate from the haptophyte ancestor of the fucoxanthin plastid, the peridinin-containing ancestor of the dinoflagellate host, and/or from lateral gene transfers. However, the evolutionary composition of fucoxanthin plastid proteomes across the diversity of kareniacean dinoflagellates remains poorly understood. Here, we determine the total composition of the plastid proteomes of seven distantly-related kareniacean dinoflagellates, including newly-sequenced members of three genera (Karenia, Karlodinium, andTakayama). Using a custom plastid-targeting predictor, automatic single-gene tree building and phylogenetic sorting of plastid-targeted proteins, we project relatively limited (~10%) and functionally distinctive contributions of the haptophyte endosymbiont to the fucoxanthin plastid proteome, in comparison to plastid-targeted proteins of dinoflagellate host origin. Considering a concatenated multigene phylogeny of haptophyte-derived plastid proteins, we show that the haptophyte order Chrysochromulinales is the closest living relative of the fucoxanthin plastid donor. We additionally perform detailed analyses of the N-terminal targeting sequences of kareniacean plastid signal peptides, reporting a surprisingly high sequence conservation. Finally, considering planetary-scale distributions of key kareniacean genera and haptophyte orders fromTaraOceans, we suggest ecological and mechanistic factors accompanying the endosymbiotic acquisition of the fucoxanthin plastid.