bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function
Authors: Campbell Amy E , Aljabri Abdulrahman A , Hesketh Andrew , Byrne Dominic P , Bennett Hayley , Patel Sanjai , Brownridge Philip , Zacharchenko Thomas , Bucca Giselda , Eyers Patrick A , Betancourt Andrea J , Eyers Claire E , Bennett Daimark 
Published: May 2024

AbstractOrganisation of the transcription cycle is facilitated by the reversible phosphorylation of the C-terminal domain of RNA Polymerase II (RNAPII-CTD) and its accessory factors. The PNUTS-PP1 protein phosphatase is crucial for mRNA synthesis and processing, yet the complete spectrum of its physiological targets in these processes remain elusive. Here, using quantitative phosphoproteomics, we discover that Cdk11, in addition to various spliceosomal and RNA processing factors, associates with PNUTS, and that disruption of PP1-binding results in hyperphosphorylation of Cdk11 at an evolutionarily conserved Serine residue, seven amino acid residues C-terminal to DFG residues in the activation loop.In vitroexperiments reveal a role for Ser DFG+7 in modulating Cdk11 kinase activity towards RNAPII-CTD Ser5. Making use of a novel technique to conditionally disrupt PP1 binding, we show that PNUTS-PP1 normally serves to restrain Cdk11 phosphorylationin vivo. Mutational analysis shows thatcdk11is not only essential for survival but also plays a widespread role in regulating normal mRNA expression and splicing. Notably, we find that a phosphomimetic mutation incdk11exhibits distinct biological effects compared to loss ofcdk11function, including defective processing of intronic small nucleolar RNAs, diminished intronic RNA Pol II velocity, and a decrease in intergenic transcription. These findings underscore physiologically significant roles of Cdk11 dephosphorylation by PNUTS-PP1 in the regulation of mRNA transcription and processing.
Thetis cells induce food-specific Treg cell differentiation and oral tolerance
Authors: Parisotto Yollanda Franco , Cabric Vanja , Park Tyler , Akagbosu Blossom , Zhao Zihan , Lo Yun , Fisher Logan , Shibu Gayathri , Paucar Iza Yoselin A. , Leslie Christina , Brown Chrysothemis C. 
Published: May 2024

AbstractThe intestinal immune system must establish tolerance to food antigens to prevent onset of allergic and inflammatory diseases. Peripherally generated regulatory T (pTreg) cells play an essential role in suppressing inflammatory responses to allergens; however, the antigen-presenting cell (APC) that instructs food-specific pTreg cells is not known. Here, we show that antigen presentation and TGF-β activation by a subset of RORγt+antigen-presenting cells (APC), Thetis cells IV (TC IV), is required for food-induced pTreg cell differentiation and oral tolerance. By contrast, antigen presentation by dendritic cells (DCs) was dispensable for pTreg induction but required for TH1 effector responses, highlighting a division of labor between tolerogenic TCs and pro-inflammatory DCs. While antigen presentation by TCs was required for food-specific pTreg generation both in early life and adulthood, the increased abundance of TCs in the peri-weaning period was associated with a window of opportunity for enhanced pTreg differentiation. These findings establish a critical role for TCs in oral tolerance and suggest that these cells may represent a key therapeutic target for the treatment of food-associated allergic and inflammatory diseases.
Light regulates widespread plant alternative polyadenylation through the chloroplast
Authors: Guillermina Kubaczka M. , Godoy Herz Micaela A. , Chen Wei-Chun , Zheng Dinghai , Petrillo Ezequiel , Tian Bin , Kornblihtt Alberto R. 
Published: May 2024

AbstractTranscription of eukaryotic protein-coding genes generates immature mRNAs that are subjected to a series of processing events, including capping, splicing, cleavage and polyadenylation (CPA) and chemical modifications of bases. Alternative polyadenylation (APA) greatly contributes to mRNA diversity in the cell. By determining the length of the 3’ untranslated region, APA generates transcripts with different regulatory elements, such as miRNA and RBP binding sites, which can influence mRNA stability, turnover and translation. In the model plantArabidopsis thaliana, APA is involved in the control of seed dormancy and flowering. In view of the physiological importance of APA in plants, we decided to investigate the effects of light/dark conditions and compare the underlying mechanisms to those elucidated for alternative splicing (AS). We found that light controls APA in approximately 30% ofArabidopsisgenes. Similar to AS, the effect of light on APA requires functional chloroplasts, is not affected in mutants of the phytochrome and cryptochrome photoreceptor pathways and is observed in roots only when the communication with the photosynthetic tissues is not interrupted. Furthermore, mitochondrial activity is necessary for the effect of light in roots but not in shoots. However, unlike AS, coupling with transcriptional elongation does not seem to be involved since light-dependent APA regulation is neither abolished in mutants of the TFIIS transcript elongation factor nor universally affected by chromatin relaxation caused by the histone deacetylase inhibition. Instead, regulation seems to be linked to light-elicited changes in the abundance of constitutive CPA factors, also mediated by the chloroplast.
Advancing chloroplast synthetic biology through high-throughput plastome engineering ofChlamydomonas reinhardtii
Authors: Inckemann René , Chotel Tanguy , Brinkmann Cedric K. , Burgis Michael , Andreas Laura , Baumann Jessica , Sharma Priyati , Klose Melanie , Barrett James , Ries Fabian , Paczia Nicole , Glatter Timo , Willmund Felix , Mackinder Luke C. M. , Erb Tobias J. 
Published: May 2024

AbstractChloroplast synthetic biology holds promise for developing improved crops through improving the function of plastids. However, chloroplast engineering efforts face limitations due to the scarcity of genetic tools and the low throughput of plant-based systems. To address these challenges, we here establishedChlamydomonas reinhardtiias a prototyping chassis for chloroplast synthetic biology. We developed an automation workflow that enables the generation, handling, and analysis of thousands of transplastomic strains in parallel, expanded the repertoire of selection markers for chloroplast transformation, established new reporter genes, and characterized over 140 regulatory parts, including native and synthetic promoters, UTRs, and intercistronic expression elements. We integrated the system within the Phytobrick cloning standard and demonstrate several applications, including a library-based approach to develop synthetic promoter designs in plastids. Finally, we provide a proof-of-concept for prototyping novel traits in plastids by introducing a chloroplast-based synthetic photorespiration pathway and demonstrating a twofold increase in biomass production. Overall, our study advances chloroplast engineering, and provides a promising platform to rapidly prototype chloroplast manipulations before their transfer into higher plants and crops.
Network Analyses of Brain Tumor Patients’ Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions
Authors: Bumbaca Brandon , Birtwistle Marc R. , Gallo James M. 
Published: May 2024

ABSTRACTGlioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte-like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used forin silicoprotein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further testedin vitroand support cell state-directed (CSD) therapy.
High-throughput protein characterization by complementation using DNA barcoded fragment libraries
Authors: Biggs Bradley W. , Price Morgan N. , Lai Dexter , Escobedo Jasmine , Fortanel Luis , Huang Yolanda Y. , Kim Kyoungmin , Trotter Valentine V. , Kuehl Jennifer V. , Lui Lauren M. , Chakraborty Romy , Deutschbauer Adam M. , Arkin Adam P. 
Published: May 2024

AbstractOur ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we usecomplementation ofauxotrophs and DNA barcodesequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains ofEscherichia colito identify genes that complement missing biochemical activity. Although assay effectiveness ranged with respect to source genome, with 41% of expected enzymes recovered, even distantE. colirelatives likeBacillus subtilisandBacteroides thetaiotaomicronshowed success. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein on an amino acid basis. Among unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq’s utility is demonstrated, with future applications in ecology, health, and engineering.
Adhesive and mechanical properties of the glue produced by 25 Drosophila species
Authors: Monier Manon , Lorenzi Jean-Noël , Narasimha Sunitha , Borne Flora , Contremoulins Vincent , Mevel Louis , Petit Romane , El Hachem Youssef , Graner François , Courtier-Orgogozo Virginie 
Published: May 2024

AbstractDrosophila glue, a bioadhesive produced by fly larvae to attach themselves to a substrate for several days, has recently gained attention for its peculiar adhesive and mechanical properties. Although Drosophila glue production was described more than 50 years ago, a general survey of the adhesive and mechanical properties of this proteinaceous gel across Drosophila species is lacking. To measure adhesion, we present here a protocol that is robust to variations in protocol parameters, pupal age and calculation methods. We find that the glue, which covers the entire pupal surface, increases the animal rigidity and plasticity when bound to a glass slide. Our survey of pupal adhesion in 25 Drosophilidae species reveals la wide range of phenotypes, from species that produce no or little glue and adhere little, to species that produce high amounts of glue and adhere strongly. One species,D. hydei, stands out from the rest and emerges as a promising model for the development of future bioadhesives, as it has the highest detachment force per glue area and produces relatively large amounts of glue relative to its size. We also observe that species that invest more in glue tend to live in more windy and less rainy climates, suggesting that differences in pupal adhesion properties across species are shaped by ecological factors. Our present survey provides a basis for future biomimetic studies based on Drosophila glue.
N-Myc and STAT Interactor is an endometriosis suppressor
Authors: Park Yuri , Guan Xiaoming , Han Sang Jun 
Published: May 2024

AbstractIn patients with endometriosis, refluxed endometrial fragments evade host immunosurveillance, developing into endometriotic lesions. However, the mechanisms underlying this evasion have not been fully elucidated. N-Myc and STAT Interactor (NMI) have been identified as key players in host immunosurveillance, including interferon (IFN)-induced cell death signaling pathways. NMI levels are markedly reduced in the stromal cells of human endometriotic lesions due to modulation by the Estrogen Receptor beta/Histone Deacetylase 8 axis. Knocking down NMI in immortalized human endometrial stromal cells (IHESCs) led to elevated RNA levels of genes involved in cell-to-cell adhesion and extracellular matrix signaling following IFNA treatment. Furthermore, NMI knockdown inhibited IFN-regulated canonical signaling pathways, such as apoptosis mediated by Interferon Stimulated Gene Factor 3, and necroptosis upon IFNA treatment. In contrast, NMI knockdown with IFNA treatment activated non-canonical IFN-regulated signaling pathways that promote proliferation, including β-Catenin and AKT signaling. Moreover, NMI knockdown in IHESCs stimulated ectopic lesions’ growth in mouse endometriosis models. Therefore, NMI is a novel endometriosis suppressor, enhancing apoptosis and inhibiting proliferation and cell adhesion of endometrial cells upon IFN exposure.
The large GTPase Guanylate-Binding Protein-1 (GBP-1) promotes mitochondrial fission in glioblastoma
Authors: Kalb Ryan C. , Nyabuto Geoffrey O. , Morran Michael P. , Maity Swagata , Justinger Jacob S. , Nestor-Kalinoski Andrea L. , Vestal Deborah J. 
Published: May 2024

AbstractGlioblastomas (aka Glioblastoma multiforme (GBMs)) are the most deadly of the adult brain tumors. Even with aggressive treatment, the prognosis is extremely poor. The large GTPase Guanylate-Binding Protein-1 (GBP-1) contributes to the poor prognosis of GBM by promoting migration and invasion. GBP-1 is substantially localized to the cytosolic side of the outer membrane of mitochondria in GBM cells. Because mitochondrial dynamics, particularly mitochondrial fission, can drive cell migration and invasion, the potential interactions between GBP-1 and mitochondrial dynamin-related protein 1 (Drp1) were explored. Drp1 is the major driver of mitochondrial fission. While GBP-1 and Drp1 both had punctate distributions within the cytoplasm and localized to regions of the cytoplasmic side of the plasma membrane of GBM cells, the proteins were only molecularly co-localized at the mitochondria. Subcellular fractionation showed that the presence of elevated GBP-1 promoted the movement of Drp1 from the cytosol to the mitochondria. Migration of U251 cells treated with the Drp1 inhibitor, Mdivi-1, was less inhibited in the cells with elevated GBP-1. Elevated GBP-1 in GBM cells resulted in shorter and wider mitochondria, most likely from mitochondrial fission. Mitochondrial fission can drive a number of important cellular processes, including cell migration, invasion, and metastasis.Simple SummaryGlioblastomas are the most common and most aggressive adult brain tumors arising from astrocytes. Up to 60% of glioblastomas are promoted by either amplification and/or mutation of the Epidermal Growth Factor Receptor (EGFR). The large GTPase Guanylate-Binding Protein-1 (GBP-1) is one of the most robustly induced proteins following EGFR signaling in glioblastomas. How GBP-1 promotes tumor progression in glioblastomas is still under investigation. This study shows that GBP-1 promotes tumor progression by associating with Drp1 at glioblastoma mitochondria and enhancing their fission. Specifically, increased mitochondrial fission can promote tumor cell migration, invasion, and metastasis.
Genome-Wide Identification and Expression Pattern of theN-acetylserotonin deacetylase (ASDAC) Gene Family in Orchidaceae
Authors: Sun Enda , Zhao Erqiang , Li Qianqian , lu wenxiu , Jin JiaQI , Li Yingjia , Yang Chen , Chen Tingying , Mou Zongmin , Zhao Dake 
Published: May 2024

AbstractOrchids are a kind of horticultural plant with highly ornamental and medical value.N-acetylserotonin deacetylase (ASDAC) is the only reverse enzyme of the melatonin biosynthesis pathway, and plays an important role in regulating the balance of melatonin. Melatonin as a multifunctional molecule, is typically involved in plant growth and development regulation, as well as abiotic stress tolerance. Here, we aimed at identifyingASDACgenes from the orchid genome to provide valuable information for further study of the role of melatonin in orchids.In this study, a total of 7ASDACgenes were identified from the 7 orchid genome with one member in each species. The 7 orchidASDACshave an HDAC functional domain, and cluster together with functionally confirmedOsHDAC10andAtHDAC14, it shows that these members may have function ofN-acetylserotonin deacetylase. Furthermore, based on the phylogenetic, motif, and gene structure analysis, the same cluster’s orchidASDACorASDAC-like genes generally contained similar introns and motifs, suggesting the distribution pattern of exons/introns and motifs were strongly related to phylogeny on an evolutionary basis. Interestingly, homologous genes ofOsHDAC10andAtHDAC14inGastrodia elatahave low homology and not cluster together with rice andA.thaliana ASDACs, showing thatASDACgene family may lost in the holomycoheterotrophic orchids. The Ka/Ks ratios ofASDACgene pairs from lower plant to higher plant were less than one, suggested thatASDACgenes have undergone purifying selection during the evolution process.Cis-acting element analysis results showed that the promoter regions of orchidASDACgenes contained plant growth and development, phytohormone, and stress-responsive elements. Moreover, most orchidASDACswere expressed in the roots, stems, leaves, flowers, and seeds. Combinedcis-acting element and tissue expression analysis, indicating orchidASDACgenes are involved in melatonin regulation of growth and development, as well as melatonin responding to various stresses in orchids. These findings of orchidASDACgenes may provide valuable information for further study of the role of melatonin in orchids.
Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens
Authors: Monteith Katy M. , Thornhill Phoebe , Vale Pedro F. 
Published: May 2024

AbstractPathogen avoidance behaviours are often assumed to be an adaptive host defence from infection. However, there is limited experimental data on the prerequisite for this assumption: heritable, intrapopulation phenotypic variation for avoidance. We investigated trophic pathogen avoidance in 122 inbredDrosophila melanogasterlines, and in a derived outbred population. Using the FlyPAD system, we tracked the feeding choice that flies made between substrates that were either clean or contained a bacterial pathogen. We uncovered significant, but weakly heritable variation in the preference index among fly lines. However, instead of avoidance, most lines demonstrated a preference for several bacterial pathogens, showing avoidance only for extremely high bacterial concentrations. Bacterial preference was not associated with susceptibility to infection and was retained in flies with disrupted immune signalling. Phenotype-genotype association analysis indicated several novel genes (CG2321, CG2006, ptp99A) associated with increased preference for the bacterial substrate, while the amino-acid transportersobremesawas associated with greater aversion. Together with previous work showing fitness benefits of consuming high-protein diets, our results suggest that bacterial attraction may instead reflect a dietary preference for protein over carbohydrate. More work quantifying intrapopulation variation in avoidance behaviours is needed to fully assess its importance in host-pathogen evolutionary ecology.
Closely related facultative and constitutive CAM phenotypes activate different transcriptional responses upon water withholding in the subgenus Tillandsia
Authors: Crego Clara Groot , Saadain Sarah , de La Harpe Marylaure , Hess Jaqueline , Barfuss Michael H.J. , Till Walter , Lexer Christian , Paun Ovidiu 
Published: May 2024

2.AbstractThe evolutionary trajectory and genetic architecture of crassulacean acid metabolism (CAM), a water-efficient form of photosynthesis that has evolved repeatedly in the plant kingdom, remains elusive. The extent to which different CAM phenotypes share a genetic basis, forming a continuum through varying degrees of expression, or exhibit divergence and redundancy of employed genes and their expression, is still debated. The subgenusTillandsiaprovides an excellent opportunity to compare the genetic basis of different CAM forms, given its broad range of photosynthetic phenotypes. Through physiological and transcriptomic analyses of well-watered and water-limited accessions of a closely related species pair, we comprehensively characterized facultative and constitutive CAM inTillandsia. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional modulation of orthogroups related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed little similarity. Enzymes of the CAM (de)carboxylation modules exhibited shared expression patterns, though distinct orthologs of PEPC were upregulated at night in each species. Our study reveals that, while the expression of certain core CAM enzymes is shared, these species exhibit substantial divergence of CAM-related transcriptomic modulation, revealing CAM’s polygenic nature and providing a possible hypothesis for its evolvability.1.HighlightWe comprehensively characterized and compared facultative and constitutive CAM phenotypes inTillandsiabromeliads on a physiological and transcriptomic level. We found substantial divergence in CAM-related transcriptomic modulation between phenotypes, highlighting the polygenic nature of the CAM continuum.