bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-prime- and Prime-side Profiling of Pro-Pro Endopeptidase Specificity Using Synthetic Combinatorial Peptide Libraries and Mass Spectrometry
Authors: Claushuis Bart , Cordfunke Robert A. , de Ru Arnoud H. , van Angeren Jordy , Baumann Ulrich , van Veelen Peter A. , Wuhrer Manfred , Corver Jeroen , Drijfhout Jan W. , Hensbergen Paul J. 
Published: March 2024

AbstractA group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease’s function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side specificity. However, PPEP specificity is also determined by the non-prime-side residues in the substrate.To gain a more complete insight into the determinants of PPEP specificity, we characterized the non-prime- and prime-side specificity of various PPEPs using a combination of synthetic combinatorial peptide libraries and mass spectrometry. With this approach, we deepened our understanding of the P3-P3’ specificities of PPEP-1 and PPEP-2, while identifying PPEP-2’s endogenous substrate as the most optimal substrate in our library data. Furthermore, by employing the library approach, we investigated the altered specificity of mutants of PPEP-1 and PPEP-2.Additionally, we characterized a novel PPEP fromAnoxybacillus tepidamans, which we termed PPEP-4. Based on structural comparisons, we hypothesized that PPEP-4 displays a PPEP-1-like prime-side specificity, which was substantiated by the experimental data. Intriguingly, another putative PPEP fromClostridioides difficile, CD1597, did not display Pro-Pro endoproteolytic activity.Collectively, we characterized PPEP specificity in detail using our robust peptide library method and, together with additional structural information, provide more insight into the intricate mechanisms that govern protease specificity.
Overlapping roles of Arabidopsis INCURVATA11 and CUPULIFORMIS2 as Polycomb Repressive Complex 2 accessory proteins
Authors: Nadi Riad , Juan-Vicente Lucía , Lup Samuel Daniel , Fernández Yolanda , Rubio Vicente , Micol José Luis 
Published: March 2024

ABSTRACTPolycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of lysine 27 of histone H3 (H3K27me3) and plays a key role in epigenetic repression of gene expression in plants and animals. PRC2 core components have all been identified inArabidopsis thaliana, with an expanding list of accessory proteins, some of which facilitate the recruitment of PRC2 to specific targets. INCURVATA11 (ICU11) is a 2-oxoglutarate and Fe2+-dependent dioxygenase that was previously shown to be a likely PRC2 accessory protein. In Tandem Affinity Purification (TAP)-based screens for interacting partners of ICU11 and its redundant paralog CUPULIFORMIS2 (CP2), we discovered that ICU11 interacts with four PRC2 core components, including EMBRYONIC FLOWER 2 (EMF2), and with the accessory proteins EMF1, TELOMERE REPEAT BINDING 1 (TRB1), TRB2, and TRB3. CP2 did not interact with PRC2 core components, nor with TRB1, TRB2, or TRB3, but did interact with TRB4 and TRB5. Both ICU11 and CP2 interacted with the nuclear proteins NAC DOMAIN CONTAINING PROTEIN 50 (NAC050), NAC052 and COP9 SIGNALOSOME SUBUNIT 1 (CSN1). Bimolecular Fluorescence Complementation (BiFC) assays revealed that ICU11 and CP2 both interact with the PRC2 core components CURLY LEAF and SWINGER, and the accessory proteins LIKE HETEROCHROMATIN PROTEIN 1, TRB1, and TRB3. ICU11 and CP2 did not interact with each other. Beyond their phenotypes, transcriptomic profiles revealed strong similarities betweenemf2-3and the double mutanticu11-5 cp2-1, as well as with mutants in PRC2 core components. A significant proportion of the genes mis-regulated inicu11-5 cp2-1are known to harbor H3K27me3 repressive marks in the wild type. Our results provide further evidence that ICU11 acts as a PRC2 accessory protein, and strongly suggest that CP2 plays a similar role.
Transcription of damage-induced RNA inArabidopsiswas frequently initiated from DSB loci within the genic regions
Authors: Kawaguchi Kohei , Satoh Soichirou , Obokata Junichi 
Published: March 2024

AbstractDNA double-strand breaks (DSBs) are the most severe DNA lesions and need to be removed immediately to prevent loss of genomic information. Recently, it has been revealed that DSBs inducede novotranscription from the cleavage sites in various species, resulting in RNAs being referred to as damage-induced RNAs (diRNAs). While diRNA synthesis is an early event in the DNA damage response and plays an essential role in DSB repair activation, the location where diRNAs are newly generated in plant remains unclear, as does their transcriptional mechanism. Here, we performed RNA sequencing of diRNAs that emerged around all DSB loci inArabidopsis thalianaunder the expression of the exogenous restriction enzymeSbfI and observed 88 diRNAs in 360 DSB loci. Most of the detected diRNAs originated within the active genes and were transcribed from DSBs in a bidirectional manner. Furthermore, we found that diRNA elongation tends to terminate at the boundary of an endogenous gene located near DSB loci. Our results provide reliable evidence for understanding the importance ofde novotranscription at DSBs and show that diRNA is a crucial factor for successful DSB repair.
14-3-3 binding regulates Tau assembly and microtubule association
Authors: Hochmair Janine , van den Oetelaar Maxime C. M. , Diez Lisa , Lemmens Lenne J. M. , Ponce Renata , Ravatt Leandre , Franck Maximilian W. , Semenova Ekaterina , Mohapatra Satabdee , Ottmann Christian , Brunsveld Luc , Wegmann Susanne 
Published: March 2024

Abstract14-3-3 proteins are among the most abundant proteins in the brain and bind a large number of proteins in a phosphorylation dependent manner, including proteins prone to aggregate in neurodegenerative diseases. Binding of 14-3-3 is reported to facilitate the function, promote solubility, and coordinate the assembly of client proteins. For the microtubule-associated protein Tau, a neuronal client of 14-3-3, we show that phosphorylation-dependent stoichiometric binding of 14-3-3ζ dimers inhibits Tau assembling into biomolecular condensates, prevents its aggregation, and realizes efficient dissociation of Tau from microtubules. In contrast, at sub-stoichiometric 14-3-3 concentrations, multivalent electrostatic interactions promote the co-condensation of 14-3-3ζ with Tau in a phosphorylation-independent manner, offering an additional level in regulating the interactions of both proteins. These findings offer long-sought mechanistic insights into how 14-3-3 proteins regulate substrate solubility and highlight their importance for maintaining Tau protein functionality in the brain.
Undruggable oncoproteins cMyc and NMyc bind to mediator of transcription with superior high affinity
Authors: Knight Andrea , Houser Josef , Otasevic Tomas , Juran Vilem , Vybihal Vaclav , Smrcka Martin , Piskacek Martin 
Published: March 2024

AbstractThe overexpression of MYC genes is frequently found in many human cancers including adult and pediatric malignant brain tumors. Targeting MYC genes continues to be challenging due to their undruggable nature. The nine-amino-acid activation domain (9aaTAD) has been identified using our prediction algorithm in all four Yamanaka factors including c-Myc and showed to activate transcription as short peptides. We generated a set of c-Myc constructs (1-108, 69-108 and 98-108) in the N-terminal regions and tested their ability to initiate transcription. We discovered strong interactions in nanomolar scale between the 9aaTAD of c-Myc and N-Myc proteins with the KIX domain of CBP coactivator. The c-Myc 9aaTAD (region 98-108) was not overlapping with the MBII (region 128-143) and therefore represents TRRAP independent activation region. Next, we showed the 9aaTADs in human c-Myc and N-Myc conservation within the MYC family. Interestingly, the loss of the 9aaTAD in L-Myc paralogs was identified in higher metazoans suggesting the deletions had occurred in early tetrapod evolution. In summary, as c-Myc is largely intrinsically disordered protein and therefore difficult to target by small molecule inhibitors, our finding of the c-Myc 9aaTAD in complex with the KIX domain represents a promising druggable target for development of new peptide inhibitors in MYC-driven tumors.
ADMA-histones define genomic loading of Rhino at the initial step of piRNA cluster formation
Authors: Saito Raku , Ishizu Hirotsugu , Harigai Ritsuko , Murano Kensaku , Siomi Mikiko C. 
Published: March 2024

AbstractInDrosophilagerm cells, piRNAs arise from dual-strand piRNA clusters. These clusters are occupied by H3K9me3, but are transcribed from internal sites in a manner dependent on the binding of HP1 homolog Rhino to H3K9me3 on the clusters. However, how initial loading of Rhino onto the clusters occurs remains unknown. Here, we used cultured ovarian somatic cells (OSCs), which lack endogenous Rhino and Rhino stabilizer Kipferl, the absence of which renders the dual-strand clusters inert, and found that exogenous Rhino tends to bind to the ends of dual-strand clusters with asymmetric dimethylarginine histones (ADMA-histones). Depletion of the arginine methyltransferases responsible for ADMA modification affected the genomic localization of Rhino in OSCs and in the ovary. We also identified genomic regions, termed INSECTs, where ADMA-dependent Rhino propagation begins. We propose that ADMA-histones define the initial genomic loading of Rhino and stabilize Rhino−genome association during cluster formation.
A functional circadian clock regulates composition and daily bacterial load of the gut microbiome inDrosophila melanogaster
Authors: Battistolli Matteo , Varponi Irene , Romoli Ottavia , Sandrelli Federica 
Published: March 2024

AbstractWhileDrosophila melanogasterserves as a crucial model for investigating both the circadian clock and gut microbiome, our understanding of their relationship in this organism is still limited. Recent analyses suggested that theDrosophilagut microbiome modulates the host circadian tran-scriptome to minimize rapid oscillations in response to changing environments. To delve deeper into the potential relationship between the gut microbiota and circadian clock inDrosophila, we examined the composition and abundance of the gut microbiota in wild-type and arrhythmicper01flies, under 12 h:12 h light: dark (12:12 LD) and constant darkness (DD) conditions. The gut microbiota of wild-type andper01flies showed differences in composition, suggesting that theD. melanogastercircadian clock has a role in shaping the gut microbiome. In 12:12 LD and DD conditions,per01mutants showed significant daily variations in gut bacterial quantity, unlike wild-type flies. This suggests that the circadian clock inD. melanogasterplays a role in maintaining daily stability in gut microbiome load. Finally, some gut bacteria exhibited significant 24 h fluctuations in their relative abundance, which appeared independent from the fly circadian clock, suggesting that certain gut commensal bacteria inDrosophilamay possess a host-independent circadian clock.
Heterochromatin protein 1 (HP1) ofSchistosoma mansoni: non-canonical chromatin landscape and fitness effects
Authors: da Trindade Natália S. , Valentini Marilia Bergamini , Rognon Anne , Mendes Tiago Manuel Fernandes , Allegretti Silmara Marques , Grunau Christoph , Cabral Fernanda J. 
Published: March 2024

AbstractHeterochromatin protein 1 (HP1) is widespread in several organisms playing a role in control of gene expression by heterochromatin formation and maintenance of silent chromatin.Schistosoma mansoniis a human parasite that is responsible for Schistosomiasis, a tropical neglected disease in the tropical and subtropical areas in the world, where the intermediate hostBiomphalaria glabratais present. In this study we attempted to investigate if theSmHP1 is enriched inS. mansonichromatin in cercariae larvae stage, compared with another larvae stage sporocysts and it’s importance forS. mansonilife cycle progression and parasite fitness. We used ChIPmentation with commercial antibody ab109028 that passed in-house quality control. Our data show thatS. mansoniHP1 enrichment is non-canonical with a peak at the transcription end sites of protein coding genes. We did not find strong differences inSmHP1 chromatin landscapes between sporocysts and cercariae. Knock-down ofSmHP1 in schistosomula andin vivoexperiments in mice unexpectedly increased parasite fitness. Our results suggest thatSmHP1 may influence chromatin structure in a non-canonical way inS. mansonistages and may play a role in regulation of parasite fitness.
ONE HEALTH APPROACH ON SARS-COV-2 – USING SHEEP AS SENTINEL ANIMALS TO INCREASE FUTURE PANDEMIC PREPAREDNESS – a pilot study
Authors: Samojlović Milena , Mesquita João , Santos-Silva Sérgio , Neptin Malin , Esbjörnsson Joakim 
Published: March 2024

AbstractCoronaviruses are a family of viruses that can infect a number of species of birds and mammals with great zoonotic potential to cross species barriers and cause spill-over events. SARS-CoV-2 has been shown to cause clinical and inapparent disease and mortality in several animals cohabitating with humans. Sheep are also susceptible to SARS-CoV-2 and have potential to harbor and spread the virus, as well as develop neutralising antibodies due to similarities of virus-receptor interactions to those in humans. The main aim of this study was to investigate the prevalence of SARS-CoV-2 neutralising antibodies in sentinel animals after natural exposure to the virus. The serum samples were collected from sheep in Central Portugal, Serra da Estrela region, both prior to and during the COVID-19 pandemic. The sheep were kept on dairy farms for production of Serra da Estrela cheese, in small herds and in constant contact with farm workers. The sera were tested using already established SARS-CoV-2 pseudovirus systems for multiple SARS-CoV-2 variants including Wuhan, Delta and Omicron. Partial neutralisation activity towards Wuhan and Delta variants was observed, while neutralisating antibody escape was observed in all Omicron variants tested due to the mutations present . Our results indicate that potential SARS-CoV-2 virus cross-species transmission could have been established through contacts between people and animals on sheep farms. Using farm animals as sentinels is of great importance for implementing One Health Approach in zoonotic virus surveillance and control towards increasing future pandemic preparedness.
Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation
Authors: Raposo Ana Cláudia , Caldas Paulo , Arez Maria , Jeremias Joana , Barbosa Pedro , Sousa-Luís Rui , Água Frederico , Oxley David , Mupo Annalisa , Eckersley-Maslin Melanie , Casanova Miguel , Grosso Ana Rita , da Rocha Simão Teixeira 
Published: March 2024

ABSTRACTDuring culture, female human pluripotent stem cells (hPSCs), including human induced PSCs (hiPSCs) exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by the loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). XCI erosion, despite its common occurrence, is often overlooked by the stem cell community, hindering a complete understanding of its impact on both fundamental and translational applications of hiPSCs. Investigating erosion dynamics in female hiPSCs, our study reveals that XCI erosion is a frequent yet heterogeneous phenomenon, resulting in the reactivation of several X-linked genes. The likelihood of a gene to erode increases for those located on the short arm of the X chromosome and within H3K27me3-enriched domains. Paradoxically, genes that typically escape XCI are hypersensitive to loss of XIST RNA and XCI erosion. This implies that XIST RNA normally restrains expression levels of these genes on the Xi. Importantly, increased X-linked gene expression upon erosion does not globally impact (hydroxy)methylation levels in hiPSCs or at imprinted regions. By exploring diverse differentiation paradigms, such as trilineage commitment and cardiac differentiation, our study reveals the persistence of abnormal XCI patterns throughout differentiation. This finding has significant implications for fundamental research, translational applications, and clinical use of stem cells. We underscore the importance of raising awareness within the stem cell community regarding XCI erosion and advocate for its inclusion in comprehensive hiPSC quality control.
TheToxoplasma gondiimitochondrial transporter ABCB7 is essential for cytosolic iron-sulfur cluster biogenesis and protein translation
Authors: Maclean Andrew E. , Sloan Megan A. , Renaud Eléa A. , Demolombe Vincent , Besteiro Sébastien , Sheiner Lilach 
Published: March 2024

AbstractIron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesised de novo in cellular compartments such as the apicoplast, mitochondrion and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on transport of an intermediate from the mitochondrial pathway. An ATP binding cassette (ABC) transporter called ABCB7 is responsible for this role in numerous commonly studied organisms, but its role in the medically important apicomplexan parasites has not yet been studied. Here we identify and characterise theToxoplasma gondiiABCB7 homolog. Genetic depletion shows that it is essential for parasite growth, and that disruption triggers partial stage conversion. Characterisation of the knock-down line highlights a defect in cytosolic Fe-S cluster biogenesis leading to defects in protein translation and other pathways including DNA and RNA replication and metabolism. Our work provides support for a broad conservation of the connection between mitochondrial and cytosolic in Fe-S cluster biosynthesis and reveal its importance for parasite survival.
R6G narrows BmrA conformational spectrum for a more efficient use of ATP
Authors: Gobet A , Moissonnier L , Zarkadas E , Magnard S , Bettler E , Martin J , Terreux R , Schoehn G , Orelle C , Jault JM , Falson P , Chaptal V 
Published: March 2024

AbstractMultidrug ABC transporters harness the energy of ATP binding and hydrolysis to change conformation and thereby translocate substrates out of the cell to detoxify them. While this general access mechanism scheme is well accepted, molecular details of this interplay is still elusive. Rhodamine6G binding on a catalytic mutant of the homodimeric multidrug ABC transporter BmrA triggers a cooperative binding of ATP on the two identical nucleotide-binding-sites, otherwise Michaelian. We investigated this asymmetric behavior via a structural-enzymology approach, solving cryoEM structure of BmrA at defined ATP ratio along the enzymatic transition, highlighting the plasticity of BmrA as it undergoes the transition from inward to outward facing conformations. Analysis of continuous heterogeneity within cryoEM data and structural dynamics, revealed that Rhodamine6G narrows the conformational spectrum explored by the nucleotide-binding-domains, describing the allosteric effect of drug binding that optimizes the ATP-dependent conversion of the transporter to the outward-facing state. Following on these findings, the effect of drug-binding showed an ATPase stimulation and a maximal transport activity of the wild-type protein at the concentration-range where the allosteric transition occurs. Drug diffusion rate is the likely rate-limiting step of the reaction, while drug transport and ATPase activities are in effect uncoupled.
OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier
Authors: Marini Simone , Barquero Alexander , Wadhwani Anisha Ashok , Bian Jiang , Ruiz Jaime , Boucher Christina , Prosperi Mattia 
Published: March 2024

AbstractPortable genomic sequencers such as Oxford Nanopore’s MinION enable real-time applications in clinical and environmental health. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. Here we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases, making it ideal for running on smartphones or tablets. OCTOPUS obtains sensitivity and precision comparable to Kraken2, while dramatically decreasing (4-to 16-fold) the false positive rate, and yielding high correlation on real-word data. OCTOPUS is available along with customized databases athttps://github.com/DataIntellSystLab/OCTOPUSandhttps://github.com/Ruiz-HCI-Lab/OctopusMobile.
N-acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque
Authors: Sikdar Rakesh , Beauclaire Mai V. , Lima Bruno P. , Herzberg Mark C. , Elias Mikael H. 
Published: March 2024

AbstractN-acyl homoserine lactones (AHLs) are small diffusible signaling molecules that mediate a cell density-dependent bacterial communication system known as quorum sensing (QS). AHL-mediated QS regulates gene expression to control many critical bacterial behaviors including biofilm formation, pathogenicity, and antimicrobial resistance. Dental plaque is a complex multispecies oral biofilm formed by successive colonization of the tooth surface by groups of commensal, symbiotic, and pathogenic bacteria, which can contribute to tooth decay and periodontal diseases. While the existence and roles of AHL-mediated QS in oral microbiota have been debated, recent evidence indicates that AHLs play significant roles in oral biofilm development and community dysbiosis. The underlying mechanisms, however, remain poorly characterized. To better understand the importance of AHL signaling in dental plaque formation, we manipulated AHL signaling by adding AHL lactonases or exogenous AHL signaling molecules. We find that AHLs can be detected in dental plaque grown under 5% CO2conditions, but not when grown under anaerobic conditions, and yet anaerobic cultures are still responsive to AHLs. QS signal disruption using lactonases leads to changes in microbial population structures in both planktonic and biofilm states, changes that are dependent on the substrate preference of the used lactonase but mainly result in the increase in the abundance of commensal and pioneer colonizer species. Remarkably, the opposite manipulation, that is the addition of exogenous AHLs increases the abundance of late colonizer bacterial species. Hence, this work highlights the importance of AHL-mediated QS in dental plaque communities, its potential different roles in anaerobic and aerobic parts of dental plaque, and underscores the potential of QS interference in the control of periodontal diseases