bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vectorial Channeling as a Mechanism for Translational Control by Functional Prions and Condensates
Authors: Gu Xinyu , Schafer Nicholas P. , Wolynes Peter G. 
Published: August 2021

Translation of messenger RNA is regulated through a diverse set of RNA-binding proteins. A significant fraction of RNA-binding proteins contain prion-like domains which form functional prions. This raises the question of how prions can play a role in translational control. Local control of translation in dendritic spines by prions has been invoked in the mechanism of synaptic plasticity and memory. We show how channeling through diffusion and processive translation cooperate in highly ordered mRNA/prion aggregates as well as in less ordered mRNA/protein condensates depending on their sub-structure. We show the direction of translational control, whether it is repressive or activating, depends on the polarity of the mRNA distribution in mRNA/prion assemblies which determines whether vectorial channeling can enhance recycling of ribosomes. Our model also addresses the effect of changes of substrate concentration in assemblies that have been suggested previously to explain translation control by assemblies through the introduction of a potential of mean force biasing diffusion of ribosomes inside the assemblies. The results from the model are compared with the experimental data on translational control by two functional RNA-binding prions, CPEB involved in memory and Rim4 involved in gametogenesis.Significance StatementmRNA/protein assemblies such as functional prions and condensates are involved in locally regulating translation in eukaryotic cells. The mode of regulation depends on the structure of these assemblies. We show that the vectorial processive nature of translation can couple to transport via diffusion so as to repress or activate translation depending on the structure of the RNA protein assembly. We find that multiple factors including diffusivity changes and free energy biases in the assemblies can regulate the translation rate of mRNA by changing the balance between substrate recycling and competition between mRNAs. We mainly focus on the example of CPEB, a functional prion that has been implicated in the mechanism of synaptic plasticity of neurons and in memory.
Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and subsequent weight regain
Authors: Cottam Matthew A. , Caslin Heather L. , Winn Nathan C. , Hasty Alyssa H. 
Published: August 2021

AbstractMost individuals do not maintain weight loss, and weight regain increases cardio-metabolic risk beyond that of obesity. Adipose inflammation directly contributes to insulin resistance; however, immune-related changes that occur with weight loss and weight regain are not well understood. Single cell RNA-sequencing was completed with CITE-sequencing and biological replicates to profile changes in murine immune subpopulations following obesity, weight loss, and weight cycling. Weight loss normalized glucose tolerance, however, type 2 immune cells did not repopulate adipose following weight loss. Many inflammatory populations persisted with weight loss and increased further following weight regain. Obesity drove T cell exhaustion and broad increases in antigen presentation, lipid handing, and inflammation that persisted with weight loss and weight cycling. This work provides critical groundwork for understanding the immunological causes of weight cycling-accelerated metabolic disease. Thus, we have created an open-access interactive portal for our processed data to improve accessibility for the research community.
Molecular basis for GIGYF-TNRC6 complex assembly in miRNA-mediated translational repression
Authors: Sobti Meghna , Mead Benjamin J. , Igreja Cátia , Stewart Alastair G. , Christie Mary 
Published: August 2021

AbstractThe GIGYF proteins associate with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2-4EHP complex is recruited to its target transcripts remain unclear. Here we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domain, bridging 4EHP to Argonaute-miRNA mRNA targets. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.
CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature
Authors: Singhania Akul , Dubelko Paige , Kuan Rebecca , Chronister William D. , Muskat Kaylin , Das Jyotirmoy , Phillips Elizabeth J. , Mallal Simon A. , Seumois Grégory , Vijayanand Pandurangan , Sette Alessandro , Lerm Maria , Peters Bjoern , Lindestam Arlehamn Cecilia S. 
Published: August 2021

ABSTRACTThe century-oldMycobacterium bovisBacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. Here, we investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or aMycobacterium tuberculosis(Mtb)-derived peptide pool. Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects. The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.
Quantification of macromolecular biomass composition for constraint-based metabolic modeling
Authors: Simensen Vetle , Schulz Christian , Karlsen Emil , Bråtelund Signe , Burgos Idun , Thorfinnsdottir Lilja Brekke , García-Calvo Laura , Bruheim Per , Almaas Eivind 
Published: August 2021

AbstractGenome-scale metabolic models (GEMs) are mathematical representations of metabolism that allow for in silico simulation of metabolic phenotypes and capabilities. A prerequisite for these predictions is an accurate representation of the biomolecular composition of the cell necessary for replication and growth, implemented in GEMs as the so-called biomass objective function (BOF). The BOF contains the metabolic precursors required for synthesis of the cellular macro- and micromolecular constituents (e.g. protein, RNA, DNA), and its composition is highly dependent on the particular organism, strain, and growth condition. Despite its critical role, the BOF is rarely constructed using specific measurements of the modeled organism, drawing the validity of this approach into question. Thus, there is a need to establish robust and reliable protocols for experimental condition-specific biomass determination. Here, we address this challenge by presenting a general pipeline for biomass quantification, evaluating its performance on Escherichia coli K-12 MG1655 sampled during balanced exponential growth under controlled conditions in a batch-fermentor set-up. We significantly improve both the coverage and molecular resolution compared to previously published workflows, quantifying 91.6% of the biomass. Our measurements display great correspondence with previously reported measurements, and we were also able to detect subtle characteristics specific to the particular E. coli strain. Using the modified E. coli GEM iML1515a, we compare the feasible flux ranges of our experimentally determined BOF with the original BOF, finding that the changes in BOF coefficients considerably affect the attainable fluxes at the genome-scale.
Type I PRMTs and PRMT5 Inversely Regulate Post-Transcriptional Intron Detention
Authors: Maron Maxim I. , Casill Alyssa D. , Gupta Varun , Sidoli Simone , Query Charles C. , Gamble Matthew J. , Shechter David 
Published: August 2021

ABSTRACTProtein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed SKaTER-seq method, analysis of co-transcriptional splicing revealed that PRMT inhibition resulted in slower splicing rates. Surprisingly, altered co-transcriptional splicing kinetics correlated poorly with ultimate changes in alternative splicing of polyadenylated RNA—particularly intron retention (RI). Investigation of RI following inhibition of nascent transcription demonstrated that PRMTs inversely regulate RI post-transcriptionally. Subsequent proteomic analysis of chromatin-associated polyadenylated RNA identified aberrant binding of the Type I substrate, CHTOP, and the Type II substrate, SmB. Targeted mutagenesis of all methylarginine sites in SmD3, SmB, and SmD1 recapitulated splicing changes seen with Type II PRMT inhibition. Conversely, mutagenesis of all methylarginine sites in CHTOP recapitulated the splicing changes seen with Type I PRMT inhibition. Closer examination of subcellular fractions indicated that RI were isolated to the nucleoplasm and chromatin. Together, these data demonstrate that PRMTs regulate the post-transcriptional processing of nuclear, detained introns through Sm and CHTOP arginine methylation.
Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism
Authors: Osterman Amy , Mondragon Alfonso 
Published: August 2021

ABSTRACTTopoisomerase V is a unique topoisomerase that combines DNA repair and topoisomerase activities. The enzyme has an unusual arrangement, with a small topoisomerase domain followed by 12 tandem (HhH)2 domains, which include three AP lyase repair domains. The unusual architecture of this enzyme bears no resemblance to any other known topoisomerase. Here we present structures of topoisomerase V in complex with DNA. The structures show that the (HhH)2 domains wrap around the DNA and in this manner appear to act as a processivity factor. There is a conformational change in the protein to expose the topoisomerase active site. The DNA bends sharply to enter the active site, which melts the DNA and probably facilitates relaxation. The structures show a DNA binding mode not observed before and provide information on the way this unusual topoisomerase relaxes DNA.
Evolutionary dynamics of piRNA clusters in Drosophila
Authors: Wierzbicki Filip , Kofler Robert , Signor Sarah 
Published: August 2021

AbstractSmall RNAs produced from transposable element (TE) rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defense against selfish DNA. In animals it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat rich regions are difficult to assemble and compare. Here we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species we show that piRNA clusters are evolving rapidly. While 70-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs, and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.x
Assembly status transition offers an avenue for allosteric activity modulation of a supramolecular enzyme
Authors: Chen Yao , Xu Weiya , Yu Shuwei , Ni Kang , She Guangbiao , Ye Xiaodong , Xing Qiong , Zhao Jian , Huang Chengdong 
Published: August 2021

AbstractNature has evolved many supramolecular proteins assembled in certain, sometimes even seemingly oversophisticated, morphological manners. The rationale behind such evolutionary efforts is often poorly understood. Here we provide atomic-resolution insights into how the dynamic building of a structurally complex enzyme with higher-order symmetry offers amenability to intricate allosteric regulation. We have established the functional coupling between enzymatic activity and protein morphological states of glutamine synthetase (GS), an old multi-subunit enzyme essential for cellular nitrogen metabolism. Cryo-EM structure determination of GS in both the catalytically active and inactive assembly states allows us to reveal an unanticipated self-assembly-induced dynamics-driven allosteric paradigm, in which the remote interactions between two subcomplex entities significantly rigidify the otherwise structurally fluctuating active sites, thereby regulating activity. We further show in vivo evidences that how the enzyme morphology transitions could be modulated by cellular factors on demand. Collectively, our data present an example of how assembly status transition offers an avenue for allosteric modulation, and sharpens our mechanistic understanding of allostery, dynamics, cooperativity, and other complex functional and regulatory properties of supramolecular enzymes.
Dysfunction of grey matter NG2 glial cells affects neuronal plasticity and behavior
Authors: Timmermann Aline , Jabs Ronald , Boehlen Anne , Domingos Catia , Skubal Magdalena , Huang Wenhui , Kirchhoff Frank , Henneberger Christian , Bilkei-Gorzo Andras , Seifert Gerald , Steinhäuser Christian 
Published: August 2021

AbstractNG2 glia represent a distinct type of macroglial cells in the CNS and are unique among glia because they receive synaptic input from neurons. They are abundantly present in white and grey matter. While the majority of white matter NG2 glia differentiates into oligodendrocytes, the physiological impact of grey matter NG2 glia and their synaptic input are ill defined yet. Here we asked whether dysfunctional NG2 glia affect neuronal signaling and behavior. We generated mice with inducible deletion of the K+ channel Kir4.1 in NG2 glia and performed comparative electrophysiological, immunohistochemical, molecular and behavioral analyses. Focussing on the hippocampus, we found that loss of the Kir4.1 potentiated synaptic depolarizations of NG2 glia and enhanced the expression of myelin basic protein. Notably, while mice with targeted deletion of the K+ channel in NG2 glia showed impaired long term potentiation at CA3-CA1 synapses, they demonstrated improved spatial memory as revealed by testing new object location recognition. Our data demonstrate that proper NG2 glia function is critical for normal brain function and behavior.
Small disulfide loops in peptide hormones mediate self-aggregation and secretory granule sorting
Authors: Reck Jennifer , Beuret Nicole , Demirci Erhan , Prescianotto-Baschong Cristina , Spiess Martin 
Published: August 2021

ABSTRACTUnlike constitutively secreted proteins, peptide hormones are stored in densely packed secretory granules, before regulated release upon stimulation. Secretory granules are formed at the trans-Golgi network (TGN) by self-aggregation of prohormones as functional amyloids. The nonapeptide hormone vasopressin, which forms a small disulfide loop, was shown to be responsible for granule formation of its precursor in the TGN as well as for toxic fibrillar aggregation of unfolded mutants in the endoplasmic reticulum (ER). Several other hormone precursors also contain similar small disulfide loops suggesting their function as a general device to mediate aggregation for granule biogenesis. To test this hypothesis, we studied the capacity of small disulfide loops of different hormone precursors to mediate aggregation in the ER and the TGN. They indeed induced ER aggregation although to different extents in Neuro-2a and COS-1 cells. Fused to a constitutively secreted reporter protein, they also promoted sorting into secretory granules, enhanced stimulated secretion, and increased Lubrol insolubility in AtT20 cells. These results support the hypothesis that small disulfide loops act as novel signals for secretory granule biogenesis and sorting by self-aggregation.
Direct Observation of Heterogeneous Formation of Amyloid Spherulites in Real-time by Super-resolution Microscopy
Authors: Zhang Min , Pinholt Henrik D. , Zhou Xin , Bohr Søren S.-R. , Banetta Luca , Zaccone Alessio , Foderà Vito , Hatzakis Nikos S. 
Published: August 2021

AbstractThe misfolding of proteins and their aggregation in the form of fibrils or amyloid-like spherulites are involved in a spectrum of pathological abnormalities. Our current understanding of protein amyloid aggregation mechanisms has primarily relied on the use of spectrometric methods to determine the average growth rates and diffraction limited microscopes with low temporal resolution to observe the large-scale morphologies of intermediates. We developed a REal-time kinetics via binding and Photobleaching LOcalisation Microscopy (REPLOM) super-resolution method to directly observe and quantify the existence and abundance of diverse aggregate morphologies below the diffraction limit and extract their heterogeneous growth kinetics. Our results revealed that even the growth of a microscopically identical aggregates, e.g. amyloid spherulites, may follow distinct pathways. Specifically, spherulites do not exclusively grow isotropically but, surprisingly, may also grow anisotropically, following similar pathways as reported for minerals and polymers. Combining our technique with machine learning approaches, we associated growth rates to specific morphological transitions and provided energy barriers and the energy landscape at the level of single aggregate morphology. Our unifying framework for the detection and analysis of spherulite growth can be extended to other self-assembled systems characterized by a high degree of heterogeneity, disentangling the broad spectrum of diverse morphologies at the single-molecule level.
Assessing vulnerability of informal floating workers in Bangladesh before and during COVID-19 pandemic: a multi-method analysis
Authors: Alam Shafiqul , Adnan Ziaul Haq , Baten Mohammed Abdul , Bag Surajit 
Published: August 2021

PurposeGlobally, a myriad of floating workers is in grave jeopardy due to the ceasing of employment opportunities that resulted from the mobility restriction during the Covid-19. Despite the global concern, developing countries have been suffering disproportionately due to the dominance of informal workers in their labour market, posing the necessity to campaign for the immediate protection of this vulnerable population. This paper analyses various dimensions of the vulnerability of urban floating workers in the context of Covid-19 in Bangladesh. In reference to International Labour Organization's (ILO) “Decent Work” concept, this paper endeavours to examine floating workers' vulnerability using the insider-outsider framework in context to Covid-19 pandemic.Design/methodology/approachThe study was conducted in two phases. In the first phase, data were collected before the pandemic to assess the vulnerability of the informal floating workers. Later, we extended the study to the second phase during the Covid-19 pandemic to understand how pandemic affects the lives and livelihood of floating workers. In phase one, data were collected from a sample of 342 floating workers and analysed based on job security, wages, working environment, psychological wellbeing and education to understand the vulnerability of floating workers. In phase two, 20 in-depth qualitative interviews were conducted, followed by thematic analysis to explore how the pandemic affects the existing vulnerability of floating workers.FindingsVarious social protection schemes were analysed to evaluate their effectiveness in reducing the vulnerability of floating workers facing socio-economic crises. The study has found that the pandemic has multiplied the existing vulnerability of the floating workers on many fronts that include job losses, food crisis, shelter insecurity, education, social, physical and mental wellbeing. In response to the pandemic, the Government stimulus packages and Non-government Covid-19 initiatives lack the appropriate system, magnitude, and focus on protecting the floating workers in Bangladesh.Practical implicationsThis paper outlines various short-term interventions and long-term policy prescriptions to safeguard floating workers' lives and livelihood from the ongoing Corona pandemic and unforeseen uncertainties.Originality/valueThis paper is the first of its kind that aims at understanding the vulnerability of this significant workforce in Bangladesh, taking the whole picture of Government and Non-government initiatives during Covid-19.