bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Chlamydia RsbU phosphatase activity by the enolase product, phosphoenolpyruvate
Authors: Rosario Christopher , Tan Ming 
Published: May 2022

ABSTRACTThe intracellular pathogen Chlamydia temporally regulates the expression of its genes but the upstream signals that control transcription are not known. The best studied regulatory pathway is a partner switching mechanism that involves an anti-sigma factor RsbW, which inhibits transcription by binding and sequestering the sigma subunit of RNA polymerase. RsbW is itself regulated by an anti-anti-sigma factor RsbV whose phosyphorylation state is controlled by the phosphatase RsbU. In this study, we showed that Chlamydia trachomatis RsbU requires manganese or magnesium as a cofactor and dephosphorylates RsbV1 and RsbV2, which are the two chlamydial paralogs of RsbV. The gene for RsbU is adjacent to the enolase gene in a number of Chlamydia genomes, and we showed that eno and rsbU are co-transcribed from the same operon. In other bacteria, there is no known functional connection between the Rsb pathway and enolase, which is an enzyme in the glycolytic pathway. We found, however, that Chlamydia RsbU phosphatase activity was inhibited by phosphoenolpyruvate (PEP), the product of the enolase reaction, but not by 2-phosphoglycerate (2PGA), which is the substrate. These findings suggest that the enolase reaction, and more generally glucose metabolism, may provide an upstream signal that regulates transcription in Chlamydia through the RsbW pathway.IMPORTANCEThe RsbW pathway is a phosphorelay that regulates gene expression in Chlamydia but its upsteam signal has not been identified. We showed that RsbU, a phosphatase in this pathway is inhibited by phosphoenolpyruvate, which is the product of the enolase reaction. As enolase is an enzyme in the glycolytic pathway, these results reveal an unrecognized link between glucose metabolism and gene regulation in chlamydiae. Moreover, as these intracellular bacteria acquire gluose from the infected host cell, our findings suggest that glucose availability may be an external signal that controls chlamydial gene expression.
Surface-Induced cAMP Signaling Requires Multiple Features of the Pseudomonas aeruginosa Type IV Pili
Authors: Kuchma S.L. , O’Toole G.A. 
Published: May 2022

AbstractPseudomonas aeruginosa type IV pili (TFP) are important for twitching motility and biofilm formation. TFP have been implicated in surface sensing, a process whereby surface-engaged cells up-regulate synthesis of the second messenger cAMP to propagate a signaling cascade leading to biofilm initiation and repression of motility. Here we show that mutations in PilA impairing proteolytic processing of the prepilin into mature pilin as well as the disruption of essential TFP components, including the PilC platform protein and PilB assembly motor protein, fail to induce surface-dependent cAMP signaling. We show that TFP retraction by surface-engaged cells is required to induce signaling, and that the retractile motor PilT is both necessary and sufficient to power surface-specific induction of cAMP. The PilU retraction motor, in contrast, is unable to support full signaling in the absence of PilT. Finally, while we have confirmed that PilA and PilJ interact by bacterial two-hybrid analysis, our data do not support the current model that PilJ-PilA interaction drives cAMP signaling.ImportanceSurface sensing by P. aeruginosa requires TFP. TFP play a critical role in the induction of the second messenger cAMP upon surface contact; this second messenger is part of a larger cascade involved in the transition from a planktonic to biofilm lifestyle. Here we show that TFP must be deployed and actively retracted by the PilT motor for the full induction of cAMP signaling. Furthermore, the mechanism whereby TFP retraction triggers cAMP induction is not well understood, and our data argues against one of the current models in the field proposed to address this knowledge gap.
A SCID mouse model to evaluate the efficacy of antivirals against SARS-CoV-2 infection
Authors: Abdelnabi Rana , Foo Caroline S. , Kaptein Suzanne J. F. , Boudewijns Robbert , Vangeel Laura , De Jonghe Steven , Jochamns Dirk , Weynand Birgit , Neyts Johan 
Published: May 2022

AbstractAncestral SARS-CoV-2 lacks the intrinsic ability to bind to the mouse ACE2 receptor and therefore establishment of SARS-CoV-2 mouse models has been limited to the use of mouse-adapted viruses or genetically modified mice. Interestingly, some of the variants of concern, such as the beta B.1.351 variant, show an improved binding to the mouse receptor and hence better replication in different Wild type (WT) mice species. Here, we desribe the establishment of SARS-CoV-2 beta B.1.351 variant infection model in male SCID mice as a tool to assess the antiviral efficacy of potential SARS-CoV-2 small molecule inhibitors. Intranasal infection of male SCID mice with 105 TCID50 of the beta B.1.351 variant resulted in high viral loads in the lungs and moderate signs of lung pathology on day 3 post-infection (pi). Treatment of infected mice with the antiviral drugs Molnupiravir (200 mg/kg, BID) or Nirmatrelvir (300 mg/kg, BID) for 3 consecutive days significantly reduced the infectious virus titers in the lungs by 1.9 and 3.8 log10 TCID50/mg tissue, respectively and significantly improved lung pathology. Together, these data demonstrate the validity of this SCID mice/beta B.1.351 variant infection model as a convenient preclinical model for assessment of potential activity of antivirals against SARS-CoV-2.ImportanceUnlike the ancestral SARS-CoV-2 strain, the beta (B.1.351) VoC has been reported to replicate to some extent in WT mice (species C57BL/6 and BALB/c). We here demonstrate that infection of SCID mice with SARS-CoV-2 beta variant results in high viral loads in the lungs on day 3 post-infection (pi). Treatment of infected mice with the antiviral drugs Molnupiravir or Nirmatrelvir for 3 consecutive days markedly reduced the infectious virus titers in the lungs and improved lung pathology. The advantages of using this mouse model over the standard hamster infection models to assess the in vivo efficacy of small molecule antiviral drugs are (i) the use of a clinical isolate without the need to use mouse-adapted strains or genetically modified animals (ii) lower amount of the test drug is needed and (ii) more convenient housing conditions compared to bigger rodents such as hamsters.
Hydroxylation site-specific and production-dependent roles of endogenous oxysterols in cellular cholesterol homeostasis
Authors: Saito Hodaka , Sato Ryuichiro , Shimizu Makoto , Yamauchi Yoshio 
Published: May 2022

AbstractThe cholesterol metabolites oxysterols play central roles in cholesterol feedback control. They modulate the activity of two master transcription factors that control cholesterol homeostatic responses, sterol regulatory element-binding protein-2 (SREBP-2) and liver X receptor (LXR). Although the role of exogenous oxysterols has been well-established, whether endogenously synthesized oxysterols similarly control both SREBP-2 and LXR to those added exogenously remains poorly explored. Here, we carefully validate the role of oxysterols enzymatically synthesized within cells in cholesterol homeostatic responses. We first show that SREBP-2 responds more sensitively to exogenous oxysterols than LXR. We then show that endogenous 25-hydroxycholesterol (25-HC), 27-HC, and 24S-HC synthesized by CH25H, CYP27A1, and CYP46A1, respectively, suppress SREBP-2 activity at different degrees by stabilizing Insig proteins whereas 7a-HC has little impact on SREBP-2. The results explain the hydroxylation site-specific role of endogenous oxysterols. On the other hand, the expression of CH25H, CYP46A1, CYP27A1, or CYP7A1 fails to induce LXR target gene expression. We also show the 25-HC production-dependent suppression of SREBP-2 using a tetracycline-inducible CH25H expression system. Moreover, we quantitatively determine the specificity of the four cholesterol hydroxylases in living cells. Based on these results, we propose that endogenous side-chain oxysterols primarily regulate the activity of SREBP-2, not LXR.
Nanoparticle-induced augmentation of neutrophils’ phagocytosis of bacteria
Authors: Rubey Kathryn M. , Mukhitov Alexander R. , Nong Jia , Wu Jichuan , Krymskaya Vera P. , Myerson Jacob W. , Worthen G. Scott , Brenner Jacob S. 
Published: May 2022

AbstractDespite the power of antibiotics, bacterial infections remain a major killer, due to antibiotic resistance and hosts with dysregulated immune systems. We and others have been developing drug-loaded nanoparticles that home to the sites of infection and inflammation via engineered tropism for neutrophils, the first-responder leukocytes in bacterial infections. Here, we examined how a member of a broad class of neutrophil-tropic nanoparticles affects neutrophil behavior, specifically questioning whether the nanoparticles attenuate an important function, bacterial phagocytosis. We found these nanoparticles actually augment phagocytosis of non-opsonized bacteria, increasing it by ~50%. We showed this augmentation of phagocytosis is likely co-opting an evolved response, as opsonized bacteria also augment phagocytosis of non-opsonized bacteria. Enhancing phagocytosis of non-opsonized bacteria may prove particularly beneficial in two clinical situations: in hypocomplementemic patients (meaning low levels of the main bacterial opsonins, complement proteins, seen in conditions such as neonatal sepsis and liver failure) or for bacteria that are largely resistant to complement opsonization (e.g., Neisseria). Additionally, we observe that; a) prior treatment with bacteria augments neutrophil uptake of neutrophil-tropic nanoparticles; b) neutrophil-tropic nanoparticles colocalize with bacteria inside of neutrophils. The observation that neutrophil-tropic nanoparticles enhance neutrophil phagocytosis and localize with bacteria inside neutrophils suggests that these nanoparticles will serve as useful carriers for drugs to ameliorate bacterial diseases.
The Scar/WAVE complex drives normal actin protrusions without the Arp2/3 complex, but proline-rich domains are required
Authors: Buracco Simona , Singh Shashi , Claydon Sophie , Paschke Peggy , Tweedy Luke , Whitelaw Jamie , McGarry Lynn , Thomason Peter A. , Insall Robert H. 
Published: May 2022

AbstractCell migration requires the constant modification of cellular shape by reorganization of the actin cytoskeleton. The pentameric Scar/WAVE regulatory complex (WRC) is the main catalyst of pseudopod and lamellipodium formation. Its actin nucleation activity has been attributed to its ability to combine monomeric actin and Arp2/3 complex through the VCA domain of Scar/WAVE, while other regions of the complex are typically thought to mediate spatial and temporal regulation and have no direct role in actin polymerization.Here we show that the Scar/WAVE with its VCA domain deleted can still induce the formation of morphologically normal actin protrusions. Equivalent results are seen in B16-F1 mouse melanoma cells and Dictyostelium discoideum cells. This actin polymerization occurs independently of the Arp2/3 complex, whose recruitment to the leading edge is greatly reduced by the loss of the VCA domain. We also expressed Scar/WAVE with VCA and polyproline domains both deleted. In Dictyostelium cells, these were only active if WASP (which contains its own proline-rich domain) was available. Similarly, in B16-F1 cells both Abi and WAVE proline-rich domains needed to be deleted before the function of the WRC was lost. Thus we conclude that proline-rich domains play a central role in actin nucleation.Our data demonstrate a new actin nucleation mechanism of the WRC that is independent of its VCA domain and the Arp2/3 complex. We also show that proline-rich domains are more fundamental than has been thought. Together, these findings suggest a new mechanism for WRC action.
Detecting apoptosis via DODO
Authors: Zhang Ziheng , Sun Zhe , Liu Ji-Long 
Published: May 2022

ABSTRACTThe real-time detection of intracellular biological processes by coded sensors has broad application prospects. Here we develop a degron based modular reporting system: the Device of Death Operation (DODO), which can be used to detect a series of biological processes. The DODO system consists of “reporter”, “sensor” and degron. After protease activation and cleavage, the degron will be released from the fluorescent protein and eventually lead to the stabilization of the fluorescent protein. By replacing different “sensors” and “reporters”, a series of biological processes can be reported through different signals. The system can effectively report the existence of TEV. To prove this concept, we successfully apply the DODO system to report apoptosis. In addition, the reporter based on degron will help to design protease reporters other than caspase.
Evolution of reading and face circuits during the first three years of reading acquisition
Authors: Feng Xiaoxia , Monzalvo Karla , Dehaene Stanislas , Dehaene-Lambertz Ghislaine 
Published: May 2022

AbstractAlthough words and faces activate neighboring regions in the fusiform gyrus, we lack an understanding of how such category selectivity emerges during development. To investigate the organization of reading and face circuits at the earliest stage of reading acquisition, we measured the fMRI responses to words, faces, houses, and checkerboards in three groups of 60 French children: 6-year-old pre-readers, 6-year-old beginning readers and 9-year-old advanced readers. The results showed that specific responses to written words were absent prior to reading, but emerged in beginning readers, irrespective of age. Likewise, specific responses to faces were barely visible in pre-readers and continued to evolve in the 9-year-olds, yet primarily driven by age rather than by schooling. Crucially, the sectors of ventral visual cortex that become specialized for words and faces harbored their own functional connectivity prior to reading acquisition: the VWFA with left-hemispheric spoken language areas, and the FFA with the contralateral region and the amygdalae. The results support the view that reading acquisition occurs through the recycling of a pre-existing but plastic circuit which, in pre-readers, already connects the VWFA site to other distant language areas. We argue that reading acquisition does not compete with the face system directly, through a pruning of preexisting face responses, but indirectly, by hindering the slow growth of face responses in the left hemisphere, thus increasing a pre-existing right hemispheric bias.HighlightsWritten words and faces activate neighboring areas of the fusiform gyri, but their developmental trajectory is different.The growth of word-induced activation in VWFA is primarily due to schooling.The growth of face responses is primarily affected by age rather than by schooling.Word and face-related areas exhibit distinct functional connectivity even prior to reading acquisitionVWFA is initially functionally connected with left-hemisphere spoken language areas, and FFA with amygdala and contralateral FFA.
Adding a new dimension: Multi-level structure and organization of mixed-species Pseudomonas aeruginosa and Staphylococcus aureus biofilms in a 4-D wound microenvironment
Authors: Dhekane Radhika , Mhade Shreeya , Kaushik Karishma S 
Published: May 2022

ABSTRACTBiofilms in wounds typically consist of aggregates of bacteria, most often Pseudomonas aeruginosa and Staphylococcus aureus, in close association with each other and the host microenvironment. Given this, the interplay across host and microbial elements, including the biochemical and nutrient profile of the microenvironment, likely influences the structure and organization of wound biofilms. While clinical studies, in vivo and ex vivo model systems have provided insights into the distribution of P. aeruginosa and S. aureus in wounds, they are limited in their ability to provide a detailed characterization of biofilm structure and organization across the host-microbial interface. On the other hand, biomimetic in vitro systems, such as host cell surfaces and simulant media conditions, albeit reductionist, have been shown to support the co-existence of P. aeruginosa and S. aureus biofilms, with species-dependent localization patterns and interspecies interactions. Therefore, composite in vitro models that bring together key features of the wound microenvironment could provide unprecedented insights into the structure and organization of mixed-species biofilms. We have built a four-dimensional (4-D) wound microenvironment consisting of a 3-D host cell scaffold of co-cultured human epidermal keratinocytes and dermal fibroblasts, and an in vitro wound milieu (IVWM); the IVWM provides the fourth dimension that represents the biochemical and nutrient profile of the wound infection state. We leveraged this composite 4-D wound microenvironment to probe the structure of mixed-species P. aeruginosa and S. aureus biofilms across multiple levels of organization such as aggregate dimensions and biomass thickness, species co-localization and organization within the biomass, overall biomass composition and interspecies interactions. In doing so, the composite 4-D wound microenvironment platform provides multi-level insights into the structure of mixed-species biofilms, which we incorporate into the current understanding of P. aeruginosa and S. aureus organization in the wound bed.
tRNA Methylation Resolves Codon Usage Bias at the Limit of Cell Viability
Authors: Masuda Isao , Yamaki Yuka , Detroja Rajesh , Tagore Somnath , Moore Henry , Maharjan Sunita , Nakano Yuko , Christian Thomas , Matsubara Ryuma , Lowe Todd , Frenkel-Morgenstern Milana , Hou Ya-Ming 
Published: May 2022

SummaryThe codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon-usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3’-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable E. coli strain, m1G37-lacking, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lacking of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial genomes that exclusively use the major isoacceptor for survival.
Parvimonas micra, an oral pathobiont associated with colorectal cancer, epigenetically reprograms human primary intestinal epithelial cells
Authors: Bergsten Emma , Mestivier Denis , Donnadieu Francoise , Pedron Thierry , Barau Caroline , Meda Landry Tsoumtsa , Mettouchi Amel , Lemichez Emmanuel , Gorgette Olivier , Chamaillard Mathias , Vaysse Amaury , Volant Stevenn , Doukani Abiba , Sansonetti Philippe J. , Sobhani Iradj , Nigro Giulia 
Published: May 2022

SummaryRecently, an intestinal dysbiotic microbiota with enrichment in oral cavity bacteria has been described in colorectal cancer (CRC) patients. Here we characterized and investigated one of these oral pathobionts, the Gram-positive anaerobic coccusParvimonas micra.We identified two phylotypes (A and B) exhibiting different phenotypes and adhesion capabilities. We observed a strong association of phylotype A with CRC, with its higher abundance in feces and in tumoral tissue compared with the normal homologous colonic mucosa, which was associated with a distinct methylation status of patients. By developing anin vitrohypoxic co-culture system of human primary colonic cells with anaerobic bacteria, we showed thatP. micraphylotype A alters the DNA methylation profile promoters of key tumor-suppressor genes, oncogenes, and genes involved in epithelial-mesenchymal transition. In colonic mucosa of CRC patients carryingP. micraphylotype A, we found similar DNA methylations alterations, together with significant enrichment of differentially expressed genes in pathways involved in inflammation, cell adhesion, and regulation of actin cytoskeleton, providing evidence ofP. micrapossible role in the carcinogenic process.
Endoplasmic Reticulum membranes are continuously required to maintain mitotic spindle size and forces
Authors: Araújo Margarida , Tavares Alexandra , Vieira Diana V. , Telley Ivo A. , Oliveira Raquel A. 
Published: May 2022

AbstractMembrane organelle function, localization, and proper partitioning upon cell division depend on interactions with the cytoskeleton. Whether, reciprocally, membrane organelles also impact on the function of cytoskeletal elements remains less clear. Here, we show that acute disruption of the Endoplasmic Reticulum (ER) around spindle poles affects mitotic spindle size and function inDrosophilasyncytial embryos. Acute ER disruption was achieved through the inhibition of ER membrane fusion by the dominant-negative cytoplasmic domain of Atlastin. We reveal that when the ER is disrupted specifically at metaphase, mitotic spindles become smaller, despite no significant changes in microtubule dynamics. These smaller spindles are still able to mediate sister chromatid separation, yet with decreased velocity. Furthermore, by inducing mitotic exit, we found that nuclear separation and distribution are affected upon ER disruption. Our results suggest that ER integrity around spindle poles is crucial for the maintenance of mitotic spindle shape and pulling forces. Additionally, ER integrity also ensures nuclear spacing during syncytial divisions.
The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer’s disease vulnerable neurons
Authors: Rodriguez-Rodriguez Patricia , Arroyo-Garcia Luis Enrique , Li Lechuan , Tsagkogianni Christina , Wang Wei , Salas-Allende Isabella , Plautz Zakary , Cedazo-Minguez Angel , Sinha Subhash , Troyanskaya Olga , Flajolet Marc , Yao Vicky , Roussarie Jean-Pierre 
Published: May 2022

SUMMARYNeurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Here, we use a data-driven functional genomics approach to model ECII neuronsin silicoand identify the proto-oncogene DEK as a potential driver of tau pathology. By modulating DEK levels in EC neuronsin vitroandin vivo, we first validate the accuracy and cell-type specificity of our network predictions. We then show thatDeksilencing changes the inducibility of immediate early genes and alters neuron excitability, leading to dysregulation of neuronal plasticity genes. We further find that loss of function of DEK leads to tau accumulation in the soma of ECII neurons, reactivity of surrounding microglia, and eventually microglia-mediated neuron loss. This study validates a pathological gene discovery tool that opens new therapeutic avenues and sheds light on a novel pathway driving tau pathology in vulnerable neurons.