bluuebunny/crossref_metadata_2025_split huggingface dataset:
AACDB: Antigen-Antibody Complex Database — a Comprehensive Database Unlocking Insights into Interaction Interface
Authors: Zhou Yuwei , Liu Wenwen , Huang Ziru , Gou Yushu , Liu Siqi , Jiang Lixu , Yang Yue , Huang Jian 
Published: November 2024

AbstractAntibodies play a crucial role in the vertebrate immune system and have diverse biomedical applications. Understanding the intricate interactions between antibodies and antigens is an important step in drug development. However, the complex and vast nature of the data presents significant challenges in accurately identifying and comprehending these interactions. To address these challenges and enhance our understanding of the antibody-antigen interface, the Antigen-Antibody Complex Database (AACDB) has been established. The current version provides a comprehensive collection of 7,498 manually processed antigen-antibody complexes, ensuring accuracy and detail. This database not only provides rich metadata but also corrects annotation errors observed in the PDB database. Furthermore, it integrates data on antibody developability and antigen-drug target relationships, making it valuable for assisting new antibody therapies development. Notably, the database includes comprehensive paratope and epitope annotation information, thereby serving as a valuable benchmark for immunoinformatics research. The AACDB interface is designed to be user-friendly, providing researchers with powerful search and visualization tools that enable effortless querying, manipulation, and visualization of complex data. Researchers can access AACDB completely online athttp://i.uestc.edu.cn/AACDB. Regular updates are promised to ensure the timely provision of scientific and valuable information.
SAM transmethylation pathway and adenosine recycling to ATP are essential for systemic regulation and immune response
Authors: Nedbalova Pavla , Kaislerova Nikola , Chodakova Lenka , Moos Martin , Dolezal Tomas 
Published: November 2024

ABSTRACTDuring parasitoid wasp infection, activated immune cells ofDrosophila melanogasterlarvae release adenosine to conserve nutrients for immune response. S-adenosylmethionine (SAM) is a methyl group donor for most methylations in the cell and is synthesized from methionine and ATP. After methylation, SAM is converted to S-adenosylhomocysteine, which is further metabolized to adenosine and homocysteine. Here, we show that the SAM transmethylation pathway is up-regulated during immune cell activation and that the adenosine produced by this pathway in immune cells acts as a systemic signal to delayDrosophilalarval development and ensure sufficient nutrient supply to the immune system. We further show that the up-regulation of the SAM transmethylation pathway and the efficiency of the immune response also depend on the recycling of adenosine back to ATP by adenosine kinase and adenylate kinase. We therefore hypothesize that adenosine may act as a sensitive sensor of the balance between cell activity, represented by the sum of methylation events in the cell, and nutrient supply. If the supply of nutrients is insufficient for a given activity, adenosine may not be effectively recycled back into ATP and may be pushed out of the cell to serve as a signal to demand more nutrients.
Sugar phosphate-mediated inhibition of peptidoglycan precursor synthesis
Authors: Keller Megan R. , Soni Vijay , Brown Megan , Rosch Kelly M. , Saleh Anas , Rhee Kyu , Doerr Tobias 
Published: November 2024

AbstractAntibiotic tolerance, the widespread ability of diverse pathogenic bacteria to sustain viability in the presence of typically bactericidal antibiotics for extended time periods, is an understudied steppingstone towards antibiotic resistance. The Gram-negative pathogenVibrio cholerae, the causative agent of cholera, is highly tolerant to β-lactam antibiotics. We previously found that the disruption of glycolysis, via deletion ofpgi(vc0374, glucose-6-phosphate isomerase), resulted in significant cell wall damage and increased sensitivity towards β-lactam antibiotics. Here, we uncover the mechanism of this resulting damage. We find that glucose causes growth inhibition, partial lysis, and a damaged cell envelope in Δpgi. Supplementation with N-acetylglucosamine, but not other carbon sources (either from upper glycolysis, TCA cycle intermediates, or cell wall precursors) restored growth, re-established antibiotic resistance towards β-lactams, and recovered cellular morphology of apgimutant exposed to glucose. Targeted metabolomics revealed the cell wall precursor synthetase enzyme GlmU (vc2762, coding for the bifunctional enzyme that converts glucosamine-1P to UDP-GlcNAc) as a critical bottleneck and mediator of glucose toxicity in Δpgi.In vitroassays of GlmU revealed that sugar phosphates (primarily glucose-1-phosphate) inhibit the acetyltransferase activity of GlmU (likely competitively), resulting in compromised PG and LPS biosynthesis. These findings identify GlmU as a critical branchpoint enzyme between central metabolism and cell envelope integrity and reveal the molecular mechanism of Δpgiglucose toxicity inVibrio cholerae.ImportanceSugar-phosphate toxicity is a well characterized phenomenon that is seen within diverse bacterial species, and yet the molecular underpinnings remain elusive. We previously discovered that disruptingVibrio cholerae’sability to eat glucose (by disrupting thepgigene), also resulted in a damaged cell envelope. Upon deletion ofpgi, glucose-phosphate levels rapidly build and inhibit the enzymatic activity of GlmU, a key step of bacterial peptidoglycan precursor synthesis. GlmU inhibition causes enhanced killing by antibiotics and a pronounced cell envelope defect. Thus, GlmU serves as a prime target for novel drug development. This research opens new routes through which central metabolism and sugar-phosphate toxicity modulate antibiotic susceptibility.
Novel Library Assembly Technique for Developing Nanobodies Targeting IPNv VP2 Protein
Authors: Pino-Belmar Camila , Himelreichs Johanna , Deride Camila , Matute Tamara , Nuñez Isaac , Cazaux Severine , Federici Fernan , Moreno Karen , Rauch Genaro Soto , Munizaga Jose , Haussmann Denise , Rojas-Fernandez Alejandro , Jaime Figueroa V , Valenzuela-Nieto Guillermo 
Published: November 2024

AbstractInfectious pancreatic necrosis virus (IPNv) poses a significant threat to the global salmon farming industry, causing high mortality and economic losses. Given the limitations of traditional antibody therapies in aquaculture, we explored the development of nanobodies targeting the VP2 protein of IPNv. We developed a novel nanobody library generation method using a streamlined assembly protocol based on Type IIS restriction enzymes. This method enabled quick and efficient bacterial display library generation, and concatenated, multi-level cloning through an ingenious design in which the ligation of the first level generates a new restriction site that can be utilized in the subsequent cloning level, allowing for rapid transfer to other vectors. By combining this assembly approach with density gradient-based enrichment and high-throughput screening, we identified nanobodies that specifically recognize IPNv’s VP2 protein. Notably, the P9 clone demonstrated high specificity for IPNv in immunofluorescence assays, highlighting its diagnostic potential. Our method not only accelerates nanobody library generation but also enhances its quality and adaptability, marking a significant advancement in enhancing the responsiveness of nanobody development platforms against emerging pathogen outbreaks.
Trans-Translation inhibitors and copper synergize for enhanced antibiotic activity
Authors: Vázquez-Hernández Melissa , Uzun Huriye Deniz , Otte Mona , Schipp Lea , Senges Christoph H. R. , Heinrich Sascha , Alumasa John N. , Stepien Jennifer , Demirbas Fatih , Cignoni Paolo , Marcus-Alic Katrin , Tschulik Kristina , Krämer Ute , Günther Pomorski Thomas , Keiler Kenneth C. , Bandow Julia E. 
Published: November 2024

AbstractTrans-Translation is the most effective ribosome rescue mechanism and a compelling target for new antimicrobial agents. A recent proteomic study revealed similarities between the responses ofBacillus subtilisto the inhibitors small-molecule inhibitors oxadiazole KKL-40 and tetrazole KKL-55 and divalent cation ionophores, indicating the disturbance of metal homeostasis as potential secondary mechanism of action. Here, we report increased copper levels in KKL-40 and KKL-55-treatedB. subtilis. Both inhibitors form copper complexes that enter large unilamellar vesicles. Copper supplementation enhanced the antibacterial activity againstB. subtilisby simultaneously increasing inhibitor and copper uptake. The co-treatment ofB. subtiliswithtrans-translation inhibitors and copper concentrations normally benign fortrans-translation-competent cells, caused an immediate stalling of growth and translation, as observed at higher KKL-40 and KKL-55 concentrations without copper supplementation. Proteome analysis showed that during translation stalling cells were unable to mount an effective copper toxicity response. Taken together, the synergetic uptake of KKL-40 and KKL-55 with copper leads to a quick-onset translation stalling, preventingB. subtilisfrom counteracting the toxic effects of rapid copper influx.Significance statementThe challenge of antimicrobial resistance is growing, necessitating an exploration of novel antibiotic targets. Among these,trans-translation has attracted considerable attention due to its ubiquitous presence in bacteria as well as its role in virulence and pathogenesis. Several inhibitors oftrans-translation have been identified in a target-based screening using a whole-cell assay. However, recent proteomic profiling studies suggested that the testedtrans-translation inhibitors might have an additional mode of action. In this work, we shed light on their previously undiscovered copper ionophore activity and explore the consequences of co-treatingB. subtiliswith KKL-40 or KKL-55 and CuCl2. This co-treatment results in a rapid antibiotic influx, and, consequently to the stalling of ribosomes, translation, and bacterial growth. Simultaneously, massive amounts of copper accumulate in the cells, the toxic effects of which require a copper stress response to mitigate. However, such a response is averted by the stalled translation. Dual mechanism antibacterial agents are attractive because they are typically associated with slow emergence of resistance. A deep understanding of the complex interplay of KKL-40 and KKL-55 with metal ions will help to fully exploittrans-translation as an antibacterial target and to develop KKL-40 and KKL-55-based antibiotics into novel treatments for bacterial infections.
Clock genesperiodandtimelesscontrol synaptogenesis inDrosophilamotor terminals
Authors: Ferreiro María José , Astrada Soledad , Cantera Rafael , Ruiz Santiago 
Published: November 2024

ABSTRACTSome neurons undergo rhythmic morphological changes that persist in constant darkness and require the expression of clock genes. Flight motoneuron MN5, one of the best studied neurons ofDrosophila melanogasterexhibits several examples of this type of circadian structural plasticity. During the morning, when the fly is active, synaptic boutons are larger than during the night when the fly is resting though more synaptic boutons and synapses are observed. Here, by comparing bouton numbers at different timepoints in normal flies and in flies carrying loss-of-function mutations in clock genestimeless(tim) orperiod(per), we investigate whether the rhythmic changes in numbers of boutons and synapses require the expression of these genes. Absence oftimexpression abolished the rhythm in bouton number whereas absence ofperexpression appeared to increase the rhythm’s amplitude. This indicates that in normal flies TIM protein is necessary to drive the normal rhythm of bouton number and PER probably has a damping effect on it. In addition, it appears thattimandperexpression normally act as inhibitor of synaptogenesis because their loss-of-function mutations caused over-proliferation of synapses. Unexpectedly, TIM and PER were expressed in different cells. TIM was found in the glial sheath wrapping the motoneuron’s axon and PER was predominantly found along the axon, suggesting that the control of the rhythmic change in bouton and synapse numbers requires interactions between different cell types.
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Authors: Macadangdang Benjamin R. , Wang Yanling , Woodward Cora , Revilla Jessica I. , Shaw Bennett M. , Sasaninia Kayvan , Makanani Sara K. , Berruto Chiara , Ahuja Umesh , Miller Jeff F. 
Published: November 2024

SummaryDiversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associatedBacteroidesspecies and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show thatBacteroidesDGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched whenBacteroidesstrains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows thatBacteroidesDGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.
The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity
Authors: Gravino Matteo , Mugford Sam T. , Kreuter Nathan , Joyce Joshua , Wilson Christine , Kliot Adi , Canham James , Mathers Thomas C. , Drurey Claire , Maqbool Abbas , Martins Carlo , Saalbach Gerhard , Hogenhout Saskia A. 
Published: November 2024

AbstractChemosensory proteins (CSPs) are a conserved family present in insects and other arthropods, recognized for their critical roles in both intra- and interspecies communication. However, the functional mechanisms of these proteins remain largely unexplored. In our previous research, we identified a CSP in aphid saliva, Mp10, from the peach-potato aphidMyzus persicae, which functions as an effector protein modulating host plant immunity. Mp10 suppresses pattern recognition receptor (PRR)-triggered immunity (PTI), the first layer of plant defence, while also inducing effector-triggered immunity (ETI). In this study, we elucidate the molecular mechanisms by which Mp10 suppresses PTI. Our findings reveal that Mp10 interacts with AMSH deubiquitinase enzymes in plants, as shown by yeast two-hybrid, co-immunoprecipitation (co-IP), and FRET-FLIM assays, with these interactions predominantly localized to intracellular membranes. Mp10 was found to modulate the dynamics of membrane-bound PRR receptor kinases in plant cells. Co-IP and mass spectrometry analyses demonstrated that Mp10 and AMSH2 associate with a range of PRR kinases, PRR-associated kinases, and proteins involved in the intracellular trafficking of membrane proteins. Mp10 reduces the accumulation of these kinases at the cell surface by promoting their internalization to internal membranes, thereby dampening PTI. Supporting this, a dominant-negative catalytically inactive variant of AMSH2 also inhibits PTI. Interestingly, Mp10 orthologues from other sap-feeding hemipteran insects exhibit similar immune-suppressive activities, and our findings show that their interaction with plant AMSH proteins is conserved, indicating this immune-suppression mechanism is evolutionarily ancient.
Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps
Authors: Peng Jiaxue , Liu Xinyue , Wang Jieni , Meng Nan , Cai Runlin , Peng Yongyi , Han Yingchun , Liao Jing , Li Chengcheng , Rubin-Blum Maxim , Ma Qiao , Dong Xiyang 
Published: November 2024

AbstractQuorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum sensing is likely a key mechanism driving microbial interactions. However, the distribution, mechanisms, and ecological roles of quorum sensing in cold seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, and 18 metabolomes from 17 global cold seep sites. We identified 299,355 quorum sensing genes from the seep non-redundant gene catalog, representing 34 gene types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. These quorum sensing genes were present in 3,576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles of carbon, nitrogen, and sulfur. Phylogenetic analysis and protein domain identification highlighted the functional roles of key quorum sensing-related proteins (e.g., PDEs, CahR, RpfC/G and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression and metabolomic profiling further confirmed the activity of representative LuxI-R pairs and identified inhibitors of quorum sensing in cold seep sediments. Overall, these findings highlight complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere.
Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases
Authors: Erickson Alek G , Isaev Sergey , Artemov Artem , He Jingyan , Semsch Bettina , Murtazina Aliia , Sun Jia , Mangold Katrin , Chalou Anthi , Frisen Jonas , Ratz Michael , Andersson Emma , Kharchenko Peter V. , Adameyko Igor 
Published: November 2024

AbstractEmbryogenesis is commonly viewed through a tree model of cell differentiation, which does not adequately represent the spatiotemporal modulation of cell multipotency underlying morphogenesis. Here we develop an integrated approach, combiningin vivosingle-cell high-throughput clonal lineage tracing with machine learning, to systematically decompose continuous spectra of clonal fate biases in mouse embryos traced from neurulation until mid-gestation. The reconstructed patterns of clonal variation uncovered gene programs driving dynamic positional biasing of clonal composition during axial skeletogenesis and peripheral neurogenesis. Mosaic combinatorial perturbations targeting multiple receptors, including the Hedgehog pathway, led to novel clone types, which has implications for engineering custom cell type assemblages from well-defined progenitorsin vivo. Altogether, our work demonstrates an effective practical approach for interrogating programs guiding lineage specification.
Pathway Specific Unbinding Free Energy Profiles of Ritonavir Dissociation From HIV-1 Protease
Authors: Vig Emily , Sun Jianan , Chang Chia-en A. 
Published: November 2024

ABSTRACTInvestigation of protein-drug recognition is key in understanding drug selectivity and binding affinity. In combination, binding/unbinding free energy landscape and intermolecular interactions can be used to understand the drug binding/unbinding mechanisms. This information is vital for the development of drugs with improved efficacy and explanation of mutation effects. This study investigated the dissociation processes of ritonavir unbinding from HIV protease (HIVp). Analyzing unbinding trajectories modeled by accelerated molecular dynamics (MD) simulations, three distinct pathways, Pathways A, B, and C, were characterized. Using reduced dimensionality strategy with the principal component analysis, we carried out short classical MD runs with explicit water to sample local fluctuation during ritonavir dissociation and applied the milestoning theory to construct unbinding free energy landscape. We found that each pathway showed similar values of binding free energy, albeit Pathway A accounts for over 50 percent of dissociation trajectories. Interesting, residue-residue correlation network analysis showed that in Pathway A, a broad correlation network outside the flap region governs protein motions during ritonavir unbinding which includes residues with reported mutation effects. However, the other two pathways showed limited correlation networks where no reported mutated residues were involved, explaining the favorability of Pathway A. Guided by the free energy profile, we investigated how and why of an energy barrier and minimum and demonstrated that hydrogen bonding governed the movement of the flap regions, directly impacting the calculated energy. Our study provided a new strategy to estimate ligand binding free energy and demonstrated the importance of the transient interactions during ligand-protein dissociation pathways in understanding drug unbinding.
Encapsulation of Select Violacein Pathway Enzymes in the 1,2-Propanediol Utilization Bacterial Microcompartment to Divert Pathway Flux
Authors: Palmero Brett Jeffrey , Gamero Emily , Mangan Niall M. , Tullman-Ercek Danielle 
Published: November 2024

AbstractA continual goal in metabolic engineering is directing pathway flux to desired products and avoiding loss of pathway intermediates to competing pathways. Encapsulation of the pathway is a possible solution, as it creates a diffusion barrier between pathway intermediates and competing enzymes. It is hypothesized that bacteria use organelles known as bacterial microcompartments - proteinaceous shells encapsulating a metabolic pathway - for this purpose. We aim to determine to what degree this hypothesized benefit is conferred to encapsulated pathways. To this end, we used bacterial microcompartments to encapsulate select enzymes from the violacein pathway, which is composed of five enzymes that produce violacein as the main product and deoxyviolacein as a side product. Importantly, we studied the pathway in a cell-free context, allowing us to hold constant the concentration of unencapsulated and encapsulated enzymes and increase our control over reaction conditions. The VioE enzyme is a branch point in that it makes the precursor for both violacein and deoxyviolacein, the VioC enzyme is required for production of deoxyviolacein, and the VioD enzyme is required for violacein production. When we encapsulated VioE and VioC and left VioD unencapsulated, the product profile shifted toward deoxyviolacein and away from violacein compared to when VioC and VioD were both unencapsulated. This work provides the first fully quantitative evidence that microcompartment-based encapsulation can be used to divert pathway flux to the encapsulated pathway. It provides insight into why certain pathways are encapsulated natively and could be leveraged for metabolic engineering applications.