keyword
https://read.qxmd.com/read/38509076/dynamics-of-accessible-chromatin-regions-and-subgenome-dominance-in-octoploid-strawberry
#1
JOURNAL ARTICLE
Chao Fang, Ning Jiang, Scott J Teresi, Adrian E Platts, Gaurav Agarwal, Chad Niederhuth, Patrick P Edger, Jiming Jiang
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS)...
March 20, 2024: Nature Communications
https://read.qxmd.com/read/38489164/genome-wide-association-study-gwas-reveals-polygenic-architecture-for-limber-pine-quantitative-disease-resistance-to-white-pine-blister-rust
#2
JOURNAL ARTICLE
Jun-Jun Liu, Richard A Sniezko, Sydney Houston, Jodie Krakowski, Genoa Alger, Andy Benowicz, Robert Sissons, Arezoo Zamany, Holly Williams, Angelia Kegley, Benjamin Rancourt
Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study (GWAS). Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over four years post inoculation...
March 15, 2024: Phytopathology
https://read.qxmd.com/read/38477703/group-c-map-kinases-phosphorylate-mbd10-to-regulate-aba-induced-leaf-senescence-in-arabidopsis
#3
JOURNAL ARTICLE
Yangdan Li, Yoshiaki Kamiyama, Fuko Minegishi, Yuki Tamura, Kota Yamashita, Sotaro Katagiri, Hinano Takase, Masahiko Otani, Ryo Tojo, Gabrielle E Rupp, Takamasa Suzuki, Naoto Kawakami, Scott C Peck, Taishi Umezawa
Abscisic acid (ABA) is a phytohormone that promotes leaf senescence in response to environmental stress. We previously identified methyl CpG-binding domain 10 (MBD10) as a phosphoprotein that becomes differentially phosphorylated after ABA treatment in Arabidopsis. ABA-induced leaf senescence was delayed in mbd10 knockout plants but accelerated in MBD10-overexpressing plants, suggesting that MBD10 positively regulates ABA-induced leaf senescence. ABA-induced phosphorylation of MBD10 occurs in planta on Thr-89, and our results demonstrated that Thr-89 phosphorylation is essential for MBD10's function in leaf senescence...
March 13, 2024: Plant Journal
https://read.qxmd.com/read/38407550/engineering-anti-crispr-proteins-to-create-cas12a-protein-switches-for-activatable-genome-editing-and-viral-protease-detection
#4
JOURNAL ARTICLE
Wenyuan Kang, Fei Xiao, Xi Zhu, Xinyu Ling, Shiyi Xie, Ruimiao Li, Peihang Yu, Linxin Cao, Chunyang Lei, Ye Qiu, Tao Liu, Zhou Nie
Proteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR-Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti-CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry-directed rational protein interface engineering...
February 26, 2024: Angewandte Chemie
https://read.qxmd.com/read/38369936/a-multilayered-post-gwas-analysis-pipeline-defines-functional-variants-and-target-genes-for-systemic-lupus-erythematosus-sle
#5
JOURNAL ARTICLE
Mehdi Fazel-Najafabadi, Loren L Looger, Harikrishna Reddy Rallabandi, Swapan K Nath
OBJECTIVES: Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWAS) have revealed multiple SLE susceptibility loci and associated single nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown. METHODS: Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping...
February 19, 2024: Arthritis & Rheumatology
https://read.qxmd.com/read/38278964/mapping-protein-rna-binding-in-plants-with-individual-nucleotide-resolution-uv-cross-linking-and-immunoprecipitation-plant-iclip2
#6
REVIEW
Martin Lewinski, Mirko Brüggemann, Tino Köster, Marlene Reichel, Thorsten Bergelt, Katja Meyer, Julian König, Kathi Zarnack, Dorothee Staiger
Despite crucial roles of RNA-binding proteins (RBPs) in plant physiology and development, methods for determining their transcriptome-wide binding landscape are less developed than those used in other model organisms. Cross-linking and immunoprecipitation (CLIP) methods (based on UV-mediated generation of covalent bonds between RNAs and cognate RBPs in vivo, purification of the cross-linked complexes and identification of the co-purified RNAs by high-throughput sequencing) have been applied mainly in mammalian cells growing in monolayers or in translucent tissue...
January 26, 2024: Nature Protocols
https://read.qxmd.com/read/38206199/identifying-lasr-quorum-sensors-with-improved-signal-specificity-by-mapping-the-sequence-function-landscape
#7
JOURNAL ARTICLE
Min Zeng, Biprodev Sarker, Stephen N Rondthaler, Vanessa Vu, Lauren B Andrews
Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa ...
January 11, 2024: ACS Synthetic Biology
https://read.qxmd.com/read/38194962/crd-a-de-novo-design-algorithm-for-the-prediction-of-cognate-protein-receptors-for-small-molecule-ligands
#8
JOURNAL ARTICLE
Santhosh Sankar, Sneha Vasudevan, Nagasuma Chandra
While predicting a ligand that binds to a protein is feasible with current methods, the opposite, i.e., the prediction of a receptor for a ligand remains challenging. We present an approach for predicting receptors of a given ligand that uses de novo design and structural bioinformatics. We have developed the algorithm CRD, comprising multiple modules combining fragment-based sub-site finding, a machine learning function to estimate the size of the site, a genetic algorithm that encodes knowledge on protein structures and a physics-based fitness scoring scheme...
January 2, 2024: Structure
https://read.qxmd.com/read/38064526/promoter-selectivity-of-the-rhlr-quorum-sensing-transcription-factor-receptor-in-pseudomonas-aeruginosa-is-coordinated-by-distinct-and-overlapping-dependencies-on-c4-homoserine-lactone-and-pqse
#9
JOURNAL ARTICLE
Nicholas R Keegan, Nathalie J Colón Torres, Anne M Stringer, Lia I Prager, Matthew W Brockley, Charity L McManaman, Joseph T Wade, Jon E Paczkowski
Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection of small molecule autoinducers, which facilitate the synchronous expression of genes involved in group behaviors, such as virulence factor production and biofilm formation. The Pseudomonas aeruginosa quorum sensing network consists of multiple interconnected transcriptional regulators, with the transcription factor, RhlR, acting as one of the main drivers of quorum sensing behaviors. RhlR is a LuxR-type transcription factor that regulates its target genes when bound to its cognate autoinducer, C4-homoserine lactone, which is synthesized by RhlI...
December 8, 2023: PLoS Genetics
https://read.qxmd.com/read/38058151/a-pthrp-gradient-drives-mandibular-condylar-chondrogenesis-via-runx2
#10
JOURNAL ARTICLE
C Tsutsumi-Arai, Y Arai, A Tran, M Salinas, Y Nakai, S Orikasa, W Ono, N Ono
The mandibular condylar cartilage (MCC) is an essential component of the temporomandibular joint, which orchestrates the vertical growth of the mandibular ramus through endochondral ossification with distinctive modes of cell differentiation. Parathyroid hormone-related protein (PTHrP) is a master regulator of chondrogenesis; in the long bone epiphyseal growth plate, PTHrP expressed by resting zone chondrocytes promotes chondrocyte proliferation in the adjacent layer. However, how PTHrP regulates chondrogenesis in the MCC remains largely unclear...
December 6, 2023: Journal of Dental Research
https://read.qxmd.com/read/38043654/proteome-landscape-and-interactome-of-voltage-gated-potassium-channel-1-6-kv1-6-of-the-murine-ophthalmic-artery-and-neuroretina
#11
JOURNAL ARTICLE
Natarajan Perumal, Hajime Yurugi, Katrin Dahm, Krishnaraj Rajalingam, Franz H Grus, Norbert Pfeiffer, Caroline Manicam
The voltage-gated potassium channel 1.6 (Kv1.6) plays a vital role in ocular neurovascular beds and exerts its modulatory functions via interaction with other proteins. However, the interactome and their potential roles remain unknown. Here, the global proteome landscape of the ophthalmic artery (OA) and neuroretina was mapped, followed by the determination of Kv1.6 interactome and validation of its functionality and cellular localization. Microfluorimetric analysis of intracellular [K+ ] and Western blot validated the native functionality and cellular expression of the recombinant Kv1...
December 1, 2023: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38034960/deep-learning-dynamic-allostery-of-g-protein-coupled-receptors
#12
JOURNAL ARTICLE
Hung N Do, Jinan Wang, Yinglong Miao
G-protein-coupled receptors (GPCRs) make up the largest superfamily of human membrane proteins and represent primary targets of ∼1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon the binding of positive and negative allosteric modulators (PAMs and NAMs). The mechanism of dynamic allosteric modulation in GPCRs remains unclear...
November 27, 2023: JACS Au
https://read.qxmd.com/read/37977224/mapping-immunological-and-host-receptor-binding-determinants-of-sars-cov-spike-protein-utilizing-the-qubevirus-platform
#13
JOURNAL ARTICLE
Carrie Sanders, Aristide Dzelamonyuy, Augustin Ntemafack, Nadia Alatoom, Godwin Nchinda, Millie M Georgiadis, Alain Bopda Waffo
The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C-terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525 , was found to contain the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S437-492 ...
November 15, 2023: Journal of Biological Chemistry
https://read.qxmd.com/read/37910551/a-mean-field-description-for-the-expansion-kinetics-of-activated-t-cell-populations
#14
JOURNAL ARTICLE
Ronny Straube, Brian J Schmidt
When lymphocytes encounter their cognate antigen, they become activated and undergo a limited number of cell divisions during which they differentiate into memory or effector cells or die. While the dynamics of individual cells are often heterogeneous, the expansion kinetics at the population level are highly reproducible, suggesting a mean-field description. To generate a finite division destiny, we consider two scenarios: Cells stop dividing after a certain number of iterations or their death rate increases with each cell division...
November 7, 2023: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/37873463/the-fitness-cost-of-spurious-phosphorylation
#15
David Bradley, Alexander Hogrebe, Rohan Dandage, Alexandre K Dubé, Mario Leutert, Ugo Dionne, Alexis Chang, Judit Villén, Christian R Landry
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious...
October 10, 2023: bioRxiv
https://read.qxmd.com/read/37847021/macp-bypass-variants-of-streptococcus-pneumoniae-pbp2a-suggest-a-conserved-mechanism-for-the-activation-of-bifunctional-cell-wall-synthases
#16
JOURNAL ARTICLE
Caroline Midonet, Sean Bisset, Irina Shlosman, Felipe Cava, David Z Rudner, Thomas G Bernhardt
The peptidoglycan (PG) layer protects bacteria from osmotic lysis and defines their shape. The class A penicillin-binding proteins (aPBPs) are PG synthases that possess both glycan polymerization and crosslinking activities needed for PG biogenesis. In Gram-negative bacteria, aPBPs require activation by outer membrane lipoproteins, which are thought to stimulate their cognate synthase by inducing conformational changes that promote polymerase function. How aPBPs are controlled in Gram-positive bacteria is less clear...
October 17, 2023: MBio
https://read.qxmd.com/read/37745557/allo-accurate-allocation-of-multi-mapped-reads-enables-regulatory-element-analysis-at-repeats
#17
Alexis Morrissey, Jeffrey Shi, Daniela Q James, Shaun Mahony
Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multi-mapped" reads that align equally well to multiple genomic locations. Since multi-mapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions...
September 15, 2023: bioRxiv
https://read.qxmd.com/read/37666802/genome-resolved-correlation-mapping-links-microbial-community-structure-to-metabolic-interactions-driving-methane-production-from-wastewater
#18
JOURNAL ARTICLE
Brandon Kieft, Niko Finke, Ryan J McLaughlin, Aditi N Nallan, Martin Krzywinski, Sean A Crowe, Steven J Hallam
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified...
September 4, 2023: Nature Communications
https://read.qxmd.com/read/37656621/system-wide-mapping-of-peptide-gpcr-interactions-in-c-%C3%A2-elegans
#19
JOURNAL ARTICLE
Isabel Beets, Sven Zels, Elke Vandewyer, Jonas Demeulemeester, Jelle Caers, Esra Baytemur, Amy Courtney, Luca Golinelli, İlayda Hasakioğulları, William R Schafer, Petra E Vértes, Olivier Mirabeau, Liliane Schoofs
Neuropeptides and peptide hormones are ancient, widespread signaling molecules that underpin almost all brain functions. They constitute a broad ligand-receptor network, mainly by binding to G protein-coupled receptors (GPCRs). However, the organization of the peptidergic network and roles of many peptides remain elusive, as our insight into peptide-receptor interactions is limited and many peptide GPCRs are still orphan receptors. Here we report a genome-wide peptide-GPCR interaction map in Caenorhabditis elegans...
August 31, 2023: Cell Reports
https://read.qxmd.com/read/37590419/the-mrna-stability-factor-khd4-defines-a-specific-mrna-regulon-for-membrane-trafficking-in-the-pathogen-ustilago-maydis
#20
JOURNAL ARTICLE
Srimeenakshi Sankaranarayanan, Carl Haag, Patrick Petzsch, Karl Köhrer, Anna Matuszyńska, Kathi Zarnack, Michael Feldbrügge
Fungal pathogens depend on sophisticated gene expression programs for successful infection. A crucial component is RNA regulation mediated by RNA-binding proteins (RBPs). However, little is known about the spatiotemporal RNA control mechanisms during fungal pathogenicity. Here, we discover that the RBP Khd4 defines a distinct mRNA regulon to orchestrate membrane trafficking during pathogenic development of Ustilago maydis . By establishing hyperTRIBE for fungal RBPs, we generated a comprehensive transcriptome-wide map of Khd4 interactions in vivo...
August 22, 2023: Proceedings of the National Academy of Sciences of the United States of America
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