bluuebunny/crossref_metadata_2025_split huggingface dataset:
E3 ligase Praja1 mediates ubiquitination and degradation of microtubule-associated protein Tau
Authors: Aoki Shiho , Kawasaki Kotaro , Imadegawa Kazuki , Oishi Mizuho , Asahi Toru , Onodera Wataru 
Published: June 2024

AbstractRING-H2 type E3 ligase Praja family is composed of Praja1 and Praja2, which promote the degradation of substrates through the ubiquitin-proteasome system. Both paralogs contribute to neuronal maturation and differentiation, indicating a significant role in the nervous system. Aggregation-prone proteins associated with neurodegenerative diseases, including TDP-43 and α-synuclein, are degraded and/or suppressed by Praja1. Furthermore, the expression level of theMAPTgene, which is frequently mutated in Alzheimer’s, is regulated by Praja2. While the Praja family has been shown to recognize various aggregation-prone proteins as substrates, it has not been determined whether Tau, a key protein that aggregates in tauopathies, is also recognized by Praja proteins. In this study, we show that Praja1, but not Praja2, recognizes Tau as a candidate substrate. We observed that Tau expression in human neuroblastoma SH-SY5Y cells decreased depending on the E3 ligase activity of Praja1. Furthermore, Praja1 polyubiquitinated and interacted with Tau, indicating that it is a target substrate. Next, by combining ancestral sequence reconstruction and mutational analysis, we revealed that the Praja1-Tau interaction began via deletion of the N- and C-terminal regions of Praja1, occurring just after the duplication of the Praja family in the common ancestor of placentals. Lastly, to test whether this interaction is disrupted under pathological conditions, P301L Tau was introduced, resulting in a degradation similar to that of wild-type Tau. These results reveal an unidentified mechanism of Tau proteostasis by Praja1 and may provide insight into the pathogenesis of neurodegenerative diseases, including tauopathy.
Novel Exploration Growth Quantifies Anxiety-like Behaviour in the Elevated Plus Maze
Authors: Zelko Matthew D. , Robinson Stephen R. , Hill-Yardin Elisa , Nasser Helen 
Published: June 2024

AbstractThe elevated plus maze is intended to provoke anxiety-like behaviour, which is primarily measured by the degree to which the rodent explores or avoids the risker, unenclosed arms. Measures such as arm entries and total time spent within the arm are conventionally used, but their analysis often produces inconsistent inferences about the level of anxiety-like behaviour being observed. This inconsistency occurs because the measures do not correlate with one another, raising the question of how validly they capture both the exploratory and avoidance motivations that typify anxiety-like behaviour. Given this inconsistency, we propose a new measure, novel exploration growth, that captures avoidance and exploratory behaviours within the maze. The growth of novel exploration tracks the first visit to discrete areas of the maze over time. The absolute amount of novel exploration, combined with the phasic nature of the exploration, reveals behavioural phenotypes with both avoidance and exploration quantified in a single time series. By addressing both motivations evoked by the maze through a single coherent measure, we provide a superior estimation of anxiety-like behaviour and resolve inconsistencies that arise when applying conventional measures alone.
Spatio-temporal analysis of the innate immune response to cytoplasmic dsDNA using a novel cGAMP biosensor
Authors: Smarduch S , Moreno-Velasquez SD , Dadsena S , Ilic D , Morant R , Pereira G , Binder M , García-Sáez AJ , Acebrón SP 
Published: June 2024

ABSTRACTThe cGAS-STING signalling pathway acts as gatekeeper in the innate immune response towards extrinsic and intrinsic sources of cytoplasmic double stranded DNA (dsDNA). At the core of this pathway is the cGAS-dependent production of the intra- and extra-cellular messenger 2’3’-cyclic GMP-AMP (cGAMP), which activates STING and leads to IRF3-dependent expression of cytokines and interferon. Despite its relevance to monitor viral and bacterial infections, cell death, and genome instability, the lack of specific live reporters has precluded spatio-temporal analyses of cGAS-STING signalling. Here, we generate a fluorescent cGAMP biosensor by engineering the functional interaction of activated STING and IRF3 at the Golgi. We show that cells encoding for the cGAMP biosensor react within 45 minutes, and in a time- and concentration-dependent manner to STING agonists and cGAMP. We demonstrate that the cGAMP biosensor is suitable for single cell characterisation of the dynamics of Herpes Simplex Virus 1 infection, mtDNA release upon apoptosis, and other sources of cytoplasmic dsDNA. Intriguingly, we show that STING signalling is not activated by ruptured micronuclei, suggesting that other cytosolic pattern recognition receptors underlie the interferon response upon chromosomal instability. Furthermore, we demonstrate that the biosensor sensitivity is sufficient to report microenvironmental cGAMP, allowing to analyse how STING signalling spreads through neighbouring cells, including upon viral infection. Taken together, we provide a tool to easily monitor the activation cGAS-STING signalling pathway by live cell imaging, plate reader or immunofluorescence analyses; and to capture the spatio-temporal and heterogenous dynamics of the response to cGAMP.
Structural Insight into the Function of Human Peptidyl Arginine Deiminase 6
Authors: Williams Jack P. C. , Mouilleron Stephane , Hernandez Trapero Rolando , Bertran M. Teresa , Marsh Joseph A. , Walport Louise J. 
Published: June 2024

AbstractPeptidyl arginine deiminase 6 (PADI6) is vital for early embryonic development in mice and humans, yet its function remains elusive. PADI6 is less conserved than other PADIs and it is currently unknown whether it has a catalytic function. Here we have shown that human PADI6 dimerises like hPADIs 2-4, however, does not bind Ca2+and is inactive inin vitroassays against standard PADI substrates. By determining the crystal structure of hPADI6, we show that hPADI6 is structured in the absence of Ca2+where hPADI2 and hPADI4 are not, and the Ca-binding sites are not conserved. Moreover, we show that whilst the key catalytic aspartic acid and histidine residues are structurally conserved, the cysteine is displaced far from the active site centre and the hPADI6 active site pocket appears closed through a unique evolved mechanism in hPADI6, not present in the other PADIs. Taken together, these findings provide insight into how the function of hPADI6 may differ from the other PADIs based on its structure and provides a resource for characterising the damaging effect of clinically significantPADI6variants.
Anoctamins mediate polymodal sensory perception and larval metamorphosis in a non-vertebrate chordate
Authors: Liang Zonglai , Hoyer Jorgen , Chatzigeorgiou Marios 
Published: June 2024

AbstractAn exceptional feature of most animals is their ability to perceive diverse sensory cues from the environment and integrate this information in their brain to yield ethologically relevant behavioral output. For the myriad of marine species, the ocean represents a complex sensory environment, which acts as a crucible of evolution for polymodal sensory perception. The cellular and molecular bases of polymodal sensory perception in a marine environment remain enigmatic.Here we use Ca2+imaging and quantitative behavioral analysis to show that in the tunicateCiona intestinalistwo members of the evolutionarily conserved Anoctamin family1–4(Tmem16E/Ano5 and Tmem16F/Ano6), are required for sensing chemosensory and mechanosensory metamorphic cues. We find that they act by modulating neuronal excitability and Ca2+response kinetics in the primary sensory neurons and axial columnar cells of the papillae, a widely conserved sensory-adhesive organ across ascidians5–9. Finally, we use electrophysiological recordings and a scramblase assay in tissue culture to demonstrate that Tmem16E/Ano5 acts as a channel, while Tmem16F/Ano6 is a bifunctional ion channel and phospholipid scramblase. Our results establish Ano5 and Ano6 as novel players in the zooplanktonic, pre-vertebrate molecular toolkit that controls polymodal sensory perception in aquatic environments.
Quorum Sensing Regulates Virulence Factors in the Coral PathogenVibrio coralliilyticus
Authors: Lydick Victoria N. , Mass Shir , Pepin Robert , Podicheti Ram , Klempic Emra , Rusch Douglas B. , Ushijima Blake , Brown Laura C. , Salomon Dor , van Kessel Julia C. 
Published: June 2024

ABSTRACTThe bacterial pathogenVibrio coralliilyticus(Vcor) causes disease in coral species worldwide. The mechanisms ofVcorcoral colonization, coral microbiome interactions, and virulence factor production are understudied. In other modelVibriospecies, virulence factors like biofilm formation, toxin secretion, and protease production are controlled through a density-dependent communication system called quorum sensing (QS). Comparative genomics indicated thatV. coralliilyticusgenomes share high sequence identity for most of the QS signaling and regulatory components identified in otherVibriospecies. Here, we identify an active QS signaling pathway in twoV. coralliilyticusstrains with distinct infection etiologies: type strain BAA-450 and coral isolate OCN008. The inter-species AI-2 autoinducer signaling pathway in both strains controls expression of the master QS transcription factor VcpR to regulate >300 genes, including protease production, biofilm formation, and two conserved type VI secretion systems (T6SSs). Activation of T6SS1 by QS results in secretion of effectors and enables interbacterial competition and killing of prey bacteria. We conclude that the QS system inV. coralliilyticusis functional and controls expression of genes involved in relevant bacterial behaviors that may influence coral infection.IMPORTANCEVibrio coralliilyticusinfects many marine organisms, including multiple species of corals, and is a primary causative agent of tissue loss diseases and bacterial-induced bleaching. Here we investigate a common cell-cell communication mechanism called quorum sensing, which is known to be intimately connected to virulence in otherVibriospecies. Our genetic and chemical studies ofV. coralliilyticusquorum sensing uncovered an active pathway that directly regulates key virulence factors: proteases, biofilms, and secretion systems. These findings connect bacterial signaling in communities to infection of corals, which may lead to novel treatments and earlier diagnoses of coral diseases in reefs.
Kinome-wide RNAi screen inCaenorhabditis elegansreveals new modulators of insulin signaling and longevity
Authors: Chamoli Manish , Foulger Anna , Singh Prachi , Lithgow Gordon , Mukhopadhyay Arnab 
Published: June 2024

AbstractThe insulin/IGF-I-like signaling (IIS) pathway is a highly conserved signaling cascade that plays a crucial role in regulating longevity across species. Given its significance in aging, identifying novel kinases interacting with the IIS pathway can provide deeper insights into the mechanisms governing longevity. In this study, we performed a targeted RNAi screen of theCaenorhabditis eleganskinome, utilizing dauer formation as a phenotypic readout. We identified several known and novel kinase modulators of the IIS pathway. These hits were enriched with both previously documented as well as undocumented lifespan regulators. Thermotolerance assays revealed mixed trends, with some kinase inhibitions increasing while others decreasing protection. We observed a positive correlation between thermotolerance and lifespan extension, as well as between dauer formation and lifespan extension, with thermotolerance proving to be a better predictor of longevity. Our findings offer a valuable resource for researchers exploring the IIS pathway and highlight novel, unannotated kinases as potential new therapeutic targets for aging interventions.
Visual neurons recognize complex image transformations
Authors: Hiramoto Masaki , Cline Hollis T. 
Published: June 2024

AbstractNatural visual scenes are dominated by sequences of transforming images. Spatial visual information is thought to be processed by detection of elemental stimulus features which are recomposed into scenes. How image information is integrated over time is unclear. We explored visual information encoding in the optic tectum. Unbiased stimulus presentation shows that the majority of tectal neurons recognize image sequences. This is achieved by temporally dynamic response properties, which encode complex image transitions over several hundred milliseconds. Calcium imaging reveals that neurons that encode spatiotemporal image sequences fire in spike sequences that predict a logical diagram of spatiotemporal information processing. Furthermore, the temporal scale of visual information is tuned by experience. This study indicates how neurons recognize dynamic visual scenes that transform over time.One-Sentence SummaryComplex visual scenes are encoded by plastic trajectories of spatiotemporal image sequences.
Unraveling CRP/cAMP-Mediated Metabolic Regulation InEscherichia coliPersister Cells
Authors: Ngo Han G. , Mohiuddin Sayed Golam , Ananda Aina , Orman Mehmet A. 
Published: June 2024

ABSTRACTA substantial gap persists in our comprehension of how bacterial metabolism undergoes rewiring during the transition to a persistent state. Also, it remains unclear which metabolic mechanisms become indispensable for persister cell survival. To address these questions, we directed our efforts towards persister cells inEscherichia colithat emerge during the late stationary phase. These cells have been recognized for their exceptional resilience and are commonly believed to be in a dormant state. Our results demonstrate that the global metabolic regulator Crp/cAMP redirects the metabolism of these antibiotic-tolerant cells from anabolism to oxidative phosphorylation. Although our data indicates that persisters exhibit a reduced metabolic rate compared to rapidly growing exponential-phase cells, their survival still relies on energy metabolism. Extensive genomic-level analyses of metabolomics, proteomics, and single-gene deletions consistently emphasize the critical role of energy metabolism, specifically the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and ATP synthase, in sustaining the viability of persisters. Altogether, this study provides much-needed clarification regarding the role of energy metabolism in antibiotic tolerance and highlights the importance of using a multipronged approach at the genomic level to obtain a broader picture of the metabolic state of persister cells.
The impact of YabG mutations onC. difficilespore germination and processing of spore substrates
Authors: Osborne Morgan S. , Brehm Joshua N. , Olivença Carmen , Cochran Alicia M. , Serrano Mónica , Henriques Adriano O. , Sorg Joseph A. 
Published: June 2024

AbstractYabG is a sporulation-specific protease that is conserved among sporulating bacteria.C. difficileYabG processes cortex destined proteins preproSleC into proSleC and CspBA to CspB and CspA. YabG also affects synthesis of spore coat/exosporium proteins CotA and CdeM. In prior work that identified CspA as the co-germinant receptor, mutations inyabGwere found which altered the co-germinants required to initiate spore germination. To understand how these mutations in theyabGlocus contribute toC. difficilespore germination, we introduced these mutations into an isogenic background. Spores derived fromC. difficile yabGC207A(catalytically inactive),C. difficile yabGA46D,C. difficile yabGG37E,andC. difficile yabGP153Lstrains germinated in response to TA alone. Recombinantly expressed and purified preproSleC incubated withE. colilysate expressing wild type YabG resulted in the removal of the pre sequence from preproSleC. Interestingly, only YabGA46Dshowed any activity towards purified preproSleC. Mutation of the YabG processing site in preproSleC (R119A) led to YabG shifting its processing to R115 or R112. Finally, changes inyabGexpression under the mutant promoters were analyzed using a SNAP-tag and revealed expression differences at early and late stages of sporulation. Overall, our results support and expand upon the hypothesis that YabG is important for germination and spore assembly and, upon mutation of the processing site, can shift where it cleaves substrates.
Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM
Authors: Renganathan Bhuvanasundar , Moore Andrew , Yeo Wei-Hong , Petruncio Alyson , Ackerman David , Wiegel Aubrey ,   The CellMap Team, Pasolli H. Amalia , Xu C. Shan , Shtengel Gleb , Hess Harald F. , Serpinskaya Anna S , Zhang Hao F. , Lippincott-Schwartz Jennifer , Gelfand Vladimir I. 
Published: June 2024

AbstractVimentin intermediate filaments (VIFs) form complex, tight-packed networks; due to this density, traditional ensemble labeling and imaging approaches cannot accurately discern single filament behavior. To address this, we introduce a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics. This technique confirmed known long-range dynein and kinesin transport of peripheral VIFs and uncovered extensive bidirectional VIF motion within the perinuclear vimentin network, a region we had thought too densely bundled to permit such motility. To examine the nanoscale organization of perinuclear vimentin, we acquired high-resolution electron microscopy volumes of a vitreously frozen cell and reconstructed VIFs and microtubules within a ∼50 µm3window. Of 583 VIFs identified, most were integrated into long, semi-coherent bundles that fluctuated in width and filament packing density. Unexpectedly, VIFs displayed minimal local co-alignment with microtubules, save for sporadic cross-over sites that we predict facilitate cytoskeletal crosstalk. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first timeSummarySingle-particle tracking demonstrates that individual filaments in bundles of vimentin intermediate filaments are transported in the cytoplasm by motor proteins along microtubules. Furthermore, using 3D FIB-SEM the authors showed that vimentin filament bundles are loosely packed and co-aligned with microtubules.
A group B streptococcal type VII secreted LXG toxin mediates interbacterial competition and colonization of the female genital tract
Authors: Job Alyx M. , Doran Kelly S. , Spencer Brady L. 
Published: June 2024

AbstractGroup BStreptococcus(GBS) asymptomatically colonizes the vagina but can opportunistically ascend to the uterus and be transmitted vertically during pregnancy, resulting in neonatal pneumonia, bacteremia and meningitis. GBS is a leading etiologic agent of neonatal infection and understanding the mechanisms by which GBS persists within the polymicrobial female genital mucosa has potential to mitigate subsequent transmission and disease. Type VIIb secretion systems (T7SSb) are encoded by Firmicutes and often mediate interbacterial competition using LXG toxins that contain conserved N-termini important for secretion and variable C-terminal toxin domains that confer diverse biochemical activities. Our recent work characterized a role for the GBS T7SSb in vaginal colonization and ascending infection but the mechanisms by which the T7SSb promotes GBS persistence in this polymicrobial niche remain unknown. Herein, we investigate the GBS T7SS in interbacterial competition and GBS niche establishment in the female genital tract. We demonstrate GBS T7SS-dependent inhibition of mucosal pathobiontEnterococcus faecalisbothin vitrousing predator-prey assays andin vivoin the murine genital tract and found that a GBS LXG protein encoded within the T7SS locus (herein named groupBstreptococcalLXGToxinA) that contributes to these phenotypes. We identify BltA as a T7SS substrate that is toxic toE. coliandS. aureusupon induction of expression along with associated chaperones. Finally, we show that BltA and its chaperones contribute to GBS vaginal colonization. Altogether, these data reveal a role for a novel T7b-secreted toxin in GBS mucosal persistence and competition.ImportanceCompetition between neighboring, non-kin bacteria is essential for microbial niche establishment in mucosal environments. Gram-positive bacteria encoding T7SSb have been shown to engage in competition through export of LXG-motif containing toxins, but these have not been characterized in group BStreptococcus(GBS), an opportunistic colonizer of the polymicrobial female genital tract. Here, we show a role for GBS T7SS in competition with mucosal pathobiontEnterococcus faecalis, bothin vitroandin vivo. We further find that a GBS LXG protein contributing to this antagonism is exported by the T7SS and is intracellularly toxic to other bacteria; therefore, we have named this protein groupBstreptococcalLXGToxinA(BltA). Finally, we show that BltA and its associated chaperones promote persistence within female genital tract tissuesin vivo.These data reveal previously unrecognized mechanisms by which GBS may compete with other mucosal opportunistic pathogens to persist within the female genital tract.
One for the road: Bumble bees consume pollen at flowers
Authors: Mayberry Maggie M. , Francis Jacob S. , Burrow Jenny K. , Dall Faith E. , Bowe Michelle , Leonard Anne , Campbell Parker , Russell Avery L. 
Published: June 2024

ABSTRACTBees are the primary consumers of pollen in many ecosystems, but pollen consumption by adult bees is rarely studied, leaving a gap in our understanding of the nutritional ecology of collective foraging and pollination biology more generally. For example, while eusocial bees feed upon pollen from colony stores, whether they also consume pollen directly from flowers to meet their own needs or to assess its quality for the broader collective is unknown. We therefore captured wild bumble bee colonies (B. bimaculatusandB. griseocollis) and tested whether individual workers consumed pollen directly from flowers in a lab-based foraging assay. After confirming presence of floral pollen in worker crops (i.e., consumption at flowers), in a field setting we tested alternative hypotheses for the function of this behavior using information about the composition, abundance, and diversity of pollen found in the crops vs. pollen baskets of three species of pollen– and nectar-foraging bumble bees (Bombus bimaculatus, B. griseocollis,andB. impatiens). Consistent with the hypothesis that consuming pollen at flowers reflects sampling, total pollen quantity in crops was consistently smaller than in pollen baskets, and basket pollen tended to be a subset of that found in crops. Further, pollen foragers consumed more and different kinds of pollen than nectar foragers. Pollen consumption at flowers is thus unlikely to be purely incidental, or to substantially benefit workers nutritionally. Instead, consuming pollen directly from flowers likely allows foragers to quickly assess pollen quality before collecting it to feed the colony as whole.SIGNIFICANCE STATEMENTWhile nectar-collecting bees are classic models for the study of foraging behavior and plant-pollinator interactions, little is known about how bees assess pollen while foraging. Pollen is a critical source of protein and lipids, offered by many plant species alongside or instead of nectar. Though variation in pollen macronutrient content and secondary chemistry affect bee reproductive performance and health, whether and how foragers evaluate pollen quality is not known. We show that foraging worker bumble bees consume pollen at flowers and suggest this behavior may allow them to sample its nutritional quality. This sheds new light on the nutritional basis of plant-pollinator interactions and adds to our understanding of how bees regulate their collection of this critical resource.