Biology subjects

Wang, G.

Publications and source records attributed to Wang, G..

At least 181 records · Page 10Linked to original sources

bioRxiv2024

A wheat tandem kinase and NLR pair confers resistance to multiple fungal pathogens

Recently discovered tandem kinase proteins (TKPs) are pivotal to the innate immune systems of cereal plants, yet how they initiate plant immune responses remains unclear. This report identifies the wheat protein WTN1, a non-canonical NLR receptor featuring tandem NB-ARC domains, as crucial for WTK3-mediated disease resistance. Both WTK3 and its allelic variant Rwt4, known for conferring resistance to wheat powdery mildew and blast respectively, are capable of recognizing the blast effector PWT4, and activate WTN1 to form calcium-permeable channels, akin to ZAR1 and Sr35. This study unveils a unique plant defense mechanism wherein TKPs and associated NLRs operate as "sensor-executor" pairs against fungal pathogens. Additionally, evolutionary analyses reveal a co-evolutionary trajectory of the TKP-NLR module, highlighting their synergistic role in triggering plant immunity. One Sentence SummaryAn ancient synergistic TKP-NLR pair triggers innate immunity for multiple disease resistance in wheat.

plant biology↗

bioRxiv2024

Morphogenic, molecular, and cellular adaptations for unidirectional airflow in the chicken lung

Unidirectional airflow in the avian lung enables gas exchange during both inhalation and exhalation. The underlying developmental process and how it deviates from that of the bidirectional mammalian lung are poorly understood. Sampling key developmental stages with multiscale 3D imaging and single-cell transcriptomics, we delineate morphogenic, molecular, and cellular features that accommodate the unidirectional airflow in the chicken lung. Primary termini of hyper-elongated branches are eliminated via proximal-short and distal-long fusions, forming parabronchi. Neoform termini extend radially through parabronchial smooth muscle to form gas-exchanging alveoli. Supporting this radial alveologenesis, branch stalks halt their proximalization, defined by SOX9-SOX2 transition, and become SOX9low parabronchi. Primary and secondary vascular plexi interface with primary and neoform termini, respectively. Single-cell and Stereo-seq spatial transcriptomics reveal a third, chicken-specific alveolar cell type expressing KRT14, hereby named luminal cells. Luminal, alveolar type 2, and alveolar type 1 cells sequentially occupy concentric zones radiating from the parabronchial lumen. Our study explores the evolutionary space of lung diversification and lays the foundation for functional analysis of species-specific genetic determinants.

developmental biology↗

bioRxiv2024

Blocking Toxin Function and Modulating the Gut Microbiota: Caffeic Acid and its Derivatives as Potential Treatments for Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea that seriously threatens public health. The disruption of normal gut microbiota by the use of broad-spectrum antimicrobial agents enables C. difficile to proliferate in the colon. The emergence and prevalence of hypervirulent C. difficile strains result in increased morbidity, mortality, and high recurrence rates of CDI, thus creating a pressing need for novel therapeutics. The multi-domain toxins TcdA and TcdB are the primary determinants of CDI pathogenesis, rendering them ideal drug targets in the anti-virulence paradigm. In this study, we identified caffeic acid and its derivatives from natural compounds library as active inhibitors of TcdB via a cell-based high-throughput phenotypic screening. Further mechanistic investigations revealed that caffeic acid phenethyl ester (CAPE) could directly bind to TcdB, thus suppressing InsP6-induced autoproteolysis and inhibiting glucosyltransferase activity. CAPE treatment remarkably reduces the pathology of CDI in a murine infection model in terms of alleviated diarrhea symptoms, decreased bacterial colonization, and relieved histopathological lesions. Moreover, CAPE treatment of C. difficile-challenged mice induces a remarkable increase in the diversity and composition of the gut microbiota and alterations of gut metabolites (e.g., adenosine, D-proline, and melatonin), which might partially contribute to the therapeutic outcomes of CAPE against CDI. Our results reveal the potential of CAPE as a therapeutic for the management of CDI, or CAPE might serve as a lead compound for the development of antivirulence drugs targeting TcdB.

microbiology↗

bioRxiv2024

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

Trematodes are obligatory parasites that generally must transmit between hosts to complete their life cycle. They parasitize varying numbers of intermediate hosts (0, 1 or 2), but the evolutionary history of these strategies and the ancestral states remain unknown. We conducted the ancestral state reconstruction of the number of intermediate hosts using mitogenomic (Trematoda) and nuclear-genomic (Neodermata) topologies. Aspidogastrea was identified as the sister-group ("basal") to all other Trematoda using a range of approaches, so it is crucial for studying the evolutionary history of trematodes. However, there is only one transcriptome available for this lineage, and mitochondrial genomes (mitogenomes) remain unavailable. Herein, we sequenced mitogenomes of two aspidogastreans: Aspidogaster ijimai and Aspidogaster conchicola. As the ancestral state reconstruction analysis is topology-sensitive, we tested multiple phylogenetic strategies, comprising the outgroup selection, phylogenetic models, partitioning strategies, and topological constraints. These mitogenomic phylogenies exhibited pronounced topological instability, with Aspidogastrea resolved as the "basal" radiation in most, but not all, topologies. Based on our analyses, Cestoda was the optimal outgroup choice, and the "heterogeneous" CAT-GTR model in PhyloBayes was the optimal model choice. We inferred the time tree and conducted ancestral state reconstruction analyses using this "optimal" topology, as well as constrained mitogenomic and nuclear genomic topologies. Results were ambiguous for some lineages, but scenario that received the strongest support is the direct life cycle (no intermediate hosts) in the ancestors of Trematoda (proto-trematodes) and Aspidogastrea (proto-aspidogastreans), while the ancestor of Digenea (proto-digeneans) had two intermediate hosts. The inferred scenario indicates that host strategies are relatively plastic among trematodes, putatively comprising several independent host gains, and multiple host losses. We propose a timeline for these events and discuss the role that alternating sexual and asexual generations putatively played in the evolution of complex parasitic life histories in digeneans.

evolutionary biology↗

bioRxiv2024

Gene Expression Prediction from Histology Images via Hypergraph Neural Networks

Spatial transcriptomics reveals the spatial distribution of genes in complex tissues, providing crucial insights into biological processes, disease mechanisms, and drug development. The prediction of gene expression based on cost-effective histology images is a promising yet challenging field of research. Existing methods for gene prediction from histology images exhibit two major limitations. First, they ignore the intricate relationship between cell morphological information and gene expression. Second, these methods do not fully utilize the different latent stages of features extracted from the images. To address these limitations, we propose a novel hypergraph neural network model, HGGEP, to predict gene expressions from histology images. HGGEP includes a gradient enhancement module to enhance the models perception of cell morphological information. A lightweight backbone network extracts multiple latent stage features from the image, followed by attention mechanisms to refine the representation of features at each latent stage and capture their relations with nearby features. To explore higher-order associations among multiple latent stage features, we stack them and feed into the hypergraph to establish associations among features at different scales. Experimental results on multiple datasets from disease samples including cancers and tumor disease, demonstrate the superior performance of our HGGEP model than existing methods. Key PointsWe develop a novel histology image-based gene prediction model named HGGEP, which demonstrates high accuracy and robust performance. To reveal the intricate relationship between cell morphology and gene expression in images, we propose a gradient enhancement module, which effectively improves the models capability in perceiving cell morphology in images. HGGEP includes a hypergraph module that efficiently models higher-order associations among features across multiple latent stages, resulting in significant performance improvement.

bioinformatics↗

bioRxiv2024

Salidroside Mitigates Malignant Arrhythmias by Restoring Sodium Channel Function During Ultra-Acute Myocardial Infarction

BackgroundThe ultra-acute phase (Phase 1a) of acute myocardial infarction (AMI) is marked by a high incidence of malignant arrhythmias, often occurring during the prehospital period. Currently, there are no effective treatment options available for managing these arrhythmias at this early stage. Methods and ResultsUsing dual-channel optical mapping, we simultaneously recorded membrane potentials and calcium transients during acute myocardial infarction. Calcium transient duration maps accurately localized the infarcted region, and action potential activation time maps revealed conduction heterogeneity in the infarcted zone. Patch-clamp recordings showed that Salidroside (Sal) (1 {micro}g/mL) significantly increased sodium current density from -59.27 {+/-} 2.15 pA/pF to -83.46 {+/-} 3.19 pA/pF (P<0.01) and shifted the Nav1.5 activation curve leftward (V1/2 from -37.27 {+/-} 0.5 mV to -44.55 {+/-} 0.7 mV, P<0.01). In rat and rabbit AMI models, Sal pre-treatment reduced conduction heterogeneity and arrhythmia incidence compared to controls. Optical mapping showed improved conduction velocity and uniformity in the Sal group. ConclusionsSal restores electrophysiological function in damaged myocardium by modulating sodium currents, reducing conduction heterogeneity, and decreasing malignant arrhythmia incidence during the ultra-acute phase of AMI. These findings suggest a novel therapeutic strategy for AMI, addressing a critical unmet need in antiarrhythmic therapy. What is New?O_LIThis study identifies Salidroside (Sal) as a novel agent that enhances sodium channel currents (Nav1.5), distinguishing it from traditional antiarrhythmic drugs which primarily target potassium channels or {beta}-adrenergic receptors. Sal improves conduction uniformity in the infarcted myocardium by restoring the electrophysiological function of damaged cardiac cells, eliminating slow conduction pathways, and reducing conduction heterogeneity. C_LIO_LIThis research introduces Sal as a promising candidate for preventing and treating arrhythmias during the critical early stages of MI, potentially improving patient outcomes. Sal administration during the ultra-acute phase (phase 1a) of myocardial infarction (MI) significantly reduces the incidence of malignant arrhythmias, a critical period characterized by high extracellular potassium and increased arrhythmia risk. C_LIO_LIUtilizing calcium transient imaging and optical mapping, this study provides precise localization of ischemic regions and detailed electrophysiological characterization, offering a robust methodology for assessing therapeutic efficacy. C_LI

pharmacology and toxicology↗

bioRxiv2024

Enhanced and idiosyncratic neural representations of personally typical scenes

Previous research shows that the typicality of visual scenes (i.e., if they are good examples of a category) determines how easily they can be perceived and represented in the brain. However, the unique visual diets individuals are exposed to across their lifetimes should sculpt very personal notions of typicality. Here, we thus investigated whether scenes that are more typical to individual observers are more accurately perceived and represented in the brain. We used drawings to enable participants to describe typical scenes (e.g., a kitchen) and converted these drawings into 3D renders. These renders were used as stimuli in a scene categorization task, during which we recorded EEG. In line with previous findings, categorization was most accurate for renders resembling the typical scene drawings of individual participants. Our EEG analyses reveal two critical insights on how these individual differences emerge on the neural level: First, personally typical scenes yielded enhanced neural representations from around 200 ms after onset. Second, personally typical scenes were represented in idiosyncratic ways, with reduced dependence on high-level visual features. We interpret these findings in a predictive processing framework, where individual differences in internal models of scene categories formed through experience shape visual analysis in idiosyncratic ways.

neuroscience↗

bioRxiv2024

GlyTrait Brings Insights into Functional Glycosylation

Glycomics research often grapples with the interpretability and biological relevance of glycomics data. Using glycosylation derived traits are promising methods for more in-depth biological insights, yet no such bioinformatic tool exists for such task. Here, we developed GlyTrait, a Python-based framework designed to enhance glycomics analysis through the innovative calculation and interpretation of derived traits from N-glycome data. GlyTrait automates the derivation of biologically significant traits, shifting focus from mere glycan abundances to functional glycan properties such as branching and fucosylation. GlyTrait extends the well-established nomenclatures and definitions of derived traits in the N-glycomics community, allowing for fast exploration and analysis of N-glycome data effortlessly. Furthermore, with the well-designed formula grammar, custom derived traits could be materialized without any knowledge of coding. Besides, a two-step post-filtering process reduces information redundancy, maintaining only the most informative traits. Finally, subsequent statistical and interpretable machine learning analysis provide robust insights into the glycosylation patterns associated with disease states. This comprehensive approach not only improves the statistical power and sensitivity compared to traditional methods, but also enhances the interpretability of glycomics data. GlyTraits efficacy is demonstrated through the re-analysis of published glycoengineered CHO cell lines and visceral leishmaniasis patient data, alongside a newly conducted pilot study for hepatocellular carcinoma (HCC) N-glycan biomarker discovery. We are confident in GlyTraits potential to become an indispensable tool for the glycomics community. Significance StatementGlycomics data is often challenging to interpret and analyze for biological relevance. GlyTrait, a Python-based tool, addresses this by automatically calculating biologically significant traits from N-glycome data, focusing on functional properties like glycan branching and fucosylation rather than mere abundance. This tool enhances data interpretability, reduces redundancy through post-filtering, and employs statistical methods to uncover glycosylation patterns linked to diseases. Demonstrated on various published datasets, as well as a newly conducted pilot study with 165 samples for hepatocellular carcinoma N-glycan biomarker discovery, GlyTrait proves to be a powerful tool. It improves the understanding of glycosylation changes in conditions like cancer, thereby benefiting the glycomics community.

bioinformatics↗

bioRxiv2024

Vestigial like 4 regulates the adipogenesis of classical brown adipose tissue

Brown adipose tissue (BAT) is mammals primary non-shivering thermogenesis organ, and the molecular mechanisms regulating BAT growth and adipogenesis are largely unknown. The Hippo-YAP pathway has been well-known for controlling organ size, and Vestigial like 4 (VGLL4) is a transcriptional regulator that modulates the Hippo-YAP pathway by competing against YAP for binding to TEAD proteins. In this study, we dissected the function of VGLL4 in regulating BAT development. We generated a conventional Vgll4 mutant mouse line, in which the two Tondu (TDU) domains of VGLL4 were disrupted. We found that deletion of the TDU domains of VGLL4 resulted in perinatal lethality and paucity of the interscapular BAT. Histological and magnetic resonance imaging studies confirmed that the adipogenesis of BAT was impaired in Vgll4 mutants. Adeno-associated virus (AAV) mediated, brown adipocyte-specific overexpression of VGLL4 increased BAT volume and protected the adult male mice from acute cold stress. Genomic studies suggest that VGLL4/TEAD1 complex directly regulates the myogenic and adipogenic gene expression programs of BAT. In conclusion, our data identify VGLL4 as a previously unrecognized adipogenesis factor that regulates classical BAT development.

developmental biology↗

bioRxiv2024

scKEPLM: Knowledge enhanced large-scale pre-trained language model for single-cell transcriptomics

The success of large-scale pre-trained language models in the Natural Language Processing (NLP) domain has encouraged their adoption in genomics and single-cell biology. Developing pre-trained models using the rapidly growing single-cell transcriptomic data helps to unravel the intricate language of cells. However, current single-cell pre-trained models primarily focus on learning gene and cell representations from extensive gene expression data, failing to fully comprehend the biological significance of the gene expression patterns and cell types they identify, which leads to limited interpretability and transferability. We propose scKEPLM, a knowledge-enhanced single-cell pre-training language model integrates a biology knowledge graph into the single-cell transcriptome pre-training process. scKEPLM covers over 41 million single-cell RNA sequences and 8.9 million gene relations. Through parallel pre-training of single-cell transcriptome sequences and genetic knowledge, combined with a Gaussian cross-attention mechanism, scKEPLM precisely aligns cell semantics with genetic information, to learn more accurate and comprehensive representations of single-cell transcriptomes. The introduction of knowledge enhancement has improved the identification of important genes in cells by scKEPLM, and greatly enriched the understanding of cell function and disease mechanism. The scKEPLM model has achieved state-of-the-art performance in more than 12 downstream tasks, including gene annotation, cell annotation, and drug response prediction, demonstrating strong generalization and transferability. Further exploration of the models interpretability demonstrates its adaptability to variations in gene expression patterns within cells under various physiological or pathological conditions.

bioinformatics↗

bioRxiv2024

Hypoxia-Inducible Factor-1 activated by PIM1 assembles a non-canonical transcription complex and resultant regulon that drives progression of JAK2V617F myeloproliferative neoplasms

Hypoxia-inducible factors (HIFs) are master transcriptional regulators, central to cellular survival under limited oxygen (hypoxia) and frequently activated within malignancy. Malignant context affects the role of HIFs within oncogenesis; however, the mechanisms regulating HIF context-specificities are not well characterised. Applying the JAK2V617F (JVF) model of myeloproliferative neoplasms (MPNs), in which HIF-1 is active in normoxia (20% O2), we sought to determine whether the modality of HIF-1 activation directs its function. We identify that HIF-1 is stabilised in JVF cells downstream of STAT1/5 signalling and upregulation of PIM1: PIM1 mediates phosphorylation of HIF-1 (Thr498/Ser500) in JVF cells that inhibits proteasomal degradation. PIM1 inhibition eradicates HIF-1 from JVF cells. Applying a single-input dual-omics output chromatin interactome methodology (DOCIA), we define JVF-specific transcription cofactors and genomic redistribution of HIF-1, and a JVF-HIF-1 regulon in primary haematopoietic stem/progenitor cells. In a cohort of 172 JVF-MPN patients, we observe significant association of the JVF-HIF-1 regulon (but strikingly, not canonical HIF-1 genes) with disease severity, progression, and patient survival. Finally, we identify a core set of JVF-HIF-1 targets significantly associated with spontaneous transformation of MPNs to AML. Our findings identify that HIF-1 activation by the JVF-PIM1 axis substantially alters its function, and that this reprogramming drives MPN disease progression, restoring the potential for targeted therapies that delineate HIF-1 activity co-opted by malignancy from essential roles within physiological oxygen homeostasis. Key PointsO_LIHIF-1 activation via PIM1 in JAK2V617F-MPNs drives non-canonical transcription complex formation/function. C_LIO_LIThe JAK2V617F-HIF-1 regulon drives MPN disease progression, transformation to AML and worse patient outcomes. C_LI

cancer biology↗

bioRxiv2024

Kinetic modeling of 18F-PI-2620 binding in the brain using an image-derived input function with total-body PET

Accurate quantification of tau binding from 18F-PI-2620 PET requires kinetic modeling and an input function. Here, we implemented a non-invasive Image-derived input function (IDIF) derived using the state-of-the-art total-body uEXPLORER PET/CT scanner to quantify tau binding and tracer delivery rate from 18F-PI-2620 in the brain. Additionally, we explored the impact of scan duration on the quantification of kinetic parameters. Total-body PET dynamic data from 15 elderly participants were acquired. Time-activity curves from the grey matter regions of interest (ROIs) were fitted to the two-tissue compartmental model (2TCM) using a subject-specific IDIF derived from the descending aorta. ROI-specific kinetic parameters were estimated for different scan durations ranging from 10 to 90 minutes. Logan graphical analysis was also used to estimate the total distribution volume (VT). Differences in kinetic parameters were observed between ROIs, including significant reduction in tracer delivery rate (K1) in the medial temporal lobe. All kinetic parameters remained relatively stable after the 60-minute scan window across all ROIs, with K1 showing high stability after 30 minutes of scan duration. Excellent correlation was observed between VT estimated using 2TCM and Logan plot analysis. This study demonstrated the utility of IDIF with total-body PET in investigating 18F-PI-2620 kinetics in the brain.

neuroscience↗

bioRxiv2024

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels, and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in-situ hybridization (FISH) require sophisticated instrumentation. Here, we introduce Profiling of RNA In-situ through Single-round iMaging (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

bioengineering↗

bioRxiv2024

Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

Yellow pitaya (Selenicereus megalanthus, 2n=4x=44) breeding remains severely hindered due to lacking a reference genome. Here we report yellow pitayas high-quality chromosome-level genome assembly and link the phenotypic trait with genomic data, based on Hi-C, ATAC, and RNA-seq data of specific tissues. We declared yellow pitaya as an autotetraploid with a 7.16 Gb genome size (harboring 27,246 high confidence genes) and majorly evolved from diploid ancestors, which remains unknown. Beyond generating the genome assembly, we explored the 3D chromatin organization which revealed insights into the genome, compartments A (648 and 519), compartments B (728 and 1064), topologically associated domains-TADs (3376 and 2031), and varying numbers of structural variations (SVs) in diploid and polyploid pitaya species, respectively. Overall, TAD boundaries were enriched with the motifs of AP2, WRKY18/60/75, MYB63/116, PHL2, and GATA8 in both pitaya species. By linking the open chromatin genomic structure to function, we identified the major changes in betalains biosynthesis pathway in diploid and polyploid pitaya. Moreover, the higher genetic expression of SmeADH1 [Chr11, Compartment A (135400000 - 135500000), genes inside the TAD region (135480000 - 135520000)], and lower expression of HuDOPA [Chr11, Compartment A (87100000 - 87200000), genes inside the TAD region (87160000-87200000)] acts as a key regulator of yellow and red color on the pericarp of polyploid and diploid pitaya, respectively. In addition, higher expression of HuCYP76AD1 genes in diploid pitaya and lower expression of SmeCYP76AD1 in polyploid pitaya potentially created the difference in the oxidase process that led to the production of betacyanin and betaxanthin, respectively. Furthermore, our results revealed not only the type of motifs that play a potential role in trait patterning but we also further uncovered that motif count in TAD-boundaries may impact the gene expression within the TAD regions of diploid and polyploid pitaya. Our valuable genomic resource and comparison of 3D euchromatin architecture of diploid and polyploid pitaya species will not only aid in the advancement of molecular breeding efforts but also offer insights into the organization of genomes, SVs, compartmentalization (A and B), and TADs, which have the potential to strengthen the idea of TADs-based trait improvement to achieve global food security.

plant biology↗

bioRxiv2024

Diversification of gene expression across extremophytes and stress-sensitive species in the Brassicaceae

Plants are composed of diverse cell types that facilitate adaptations to the environment, yet cross-species comparisons of such response programs at single-cell resolution remain scarce. To explore this diversity, here we profiled >200,000 root cells from five Brassicaceae species, including stress-sensitive species (Arabidopsis thaliana, Sisymbrium irio), extremophytes (Eutrema salsugineum, Schrenkiella parvula), and the polyploid crop Camelina sativa under control, NaCl, and abscisic acid (ABA) treatments. We developed a computational pipeline to characterize the conservation and divergence of cell-type gene expression across the Brassicaceae, revealing that approximately half of previously defined Arabidopsis cell-type markers fail to maintain conserved expression in one or more non-Arabidopsis species. Therefore, we curated a refined set of pan-Brassicaceae markers and identified orthologs whose expression profiles have diverged across lineages. Using in situ hybridization, we mapped distinct cortex subpopulations to specific cortical layers across species, and found flavonoid biosynthesis programs preferentially localized to the inner cortex layer, linking cortex-layer specification to metabolic specialization. Cell-type contributions to stress responses differed among species and across treatments, with lineage-specific losses of responsiveness occurring less frequently but evolutionarily more favored than lineage-specific gains. In C. sativa, sub-genomes contributed equally to stress responses, and homeologs with divergent responses typically lacked other signatures of functional divergence. Together, this work establishes a foundational root single-cell atlas and an analytical framework for multi-species comparative transcriptomics, providing insights into how stress responses diversify across cell types, stress-sensitive to stress-adapted species, and in crop lineages.

plant biology↗

bioRxiv2024

Oligopeptide (FK)4 facilitates the determination of the absolute stereochemistry of chiral organic compounds via NMR Spectroscopy

Molecular chirality plays a crucial role in the fields of chemistry and biology. Various nuclear magnetic resonance (NMR) methods have been employed for assignment of stereochemical configurations. Alignment media for measurements of anisotropic parameters contribute to configuration elucidations, while chiral auxiliaries assist in enantiomer discrimination and chiral recognition. However, each method comes with limitations, and the assignment of absolute configuration by NMR remains challenging. In this study, we explored a combined approach for absolute configuration elucidation with the multifaceted application of the oligopeptide (FK)4, which possesses dual functionalities as an alignment medium for anisotropic NMR measurements and a chiral differentiating agent. As an alignment medium, (FK)4 facilitates the analysis of stereochemical features through residual dipolar couplings (RDC), aiding in the structural elucidation of stereoisomers. Moreover, (FK)4 exhibits unique chiral differentiating properties, interacting distinctly with enantiomers and resulting in observable bifurcation of chemical shift signals, in 13C, 1H and 19F spectra. Using isoleucine and xylose as model compounds, we demonstrate how the dual functionality of (FK)4 enables the identification of stereoisomeric structures via RDC parameters and the assignment of enantiomeric configurations through measurements of t2 relaxation time coupled with theoretical simulations. These findings highlight the potential of versatile chiral media as (FK)4 for approaching the elucidation of absolute configurations of organic molecules via combined NMR spectroscopy approaches, with implications for structural characterization and enantiomer discrimination in chemical applications.

biochemistry↗

bioRxiv2024

Inhibitor of cardiolipin biosynthesis-related enzyme MoGep4 confers broad-spectrum anti-fungal activity

Plant pathogens cause devastating diseases, leading to serious losses to agriculture. Mechanistic understanding of pathogenesis of plant pathogens lays the foundation for the development of fungicides for disease control. Mitophagy, a specific form of autophagy, is important for fungal virulence. The role of cardiolipin, mitochondrial signature phospholipid, in mitophagy and pathogenesis is largely unknown in plant pathogenic fungi. The functions of enzymes involved in cardiolipin biosynthesis and relevant inhibitors were assessed using a set of assays, including genetic deletion, plant infection, lipidomics, chemical-protein interaction, chemical inhibition, and field trials. Our results showed that the cardiolipin biosynthesis-related gene MoGEP4 of the rice blast fungus Magnaporthe oryzae regulates growth, conidiation, cardiolipin biosynthesis, and virulence. Mechanistically, MoGep4 regulated mitophagy and Mps1-MAPK phosphorylation, which are required for virulence. Chemical alexidine dihydrochloride (AXD) inhibited the enzyme activity of MoGep4, cardiolipin biosynthesis and mitophagy. Importantly, AXD efficiently inhibited the growth of 10 plant pathogens and controlled rice blast and Fusarium head blight in the field. Our study demonstrated that MoGep4 regulates mitophagy, Mps1 phosphorylation and pathogenesis in M. oryzae. In addition, we found that the MoGep4 inhibitor, AXD, displays broad-spectrum antifungal activity and is a promising candidate for fungicide development.

microbiology↗

bioRxiv2024

Studies of CrHCF244 reveal similarities and differences in psbA translation between Chlamydomonas reinhardtii and Arabidopsis thaliana

Translation of psbA, the chloroplast gene that encodes the D1 subunit of Photosystem II (PSII), is important for both PSII biogenesis and repair. The translation of the psbA transcript in the chloroplast is under the control of nuclear gene products. Using a Chlamydomonas forward genetic screen and whole genome sequencing, we found a mutant defective in PSII activity and mapped the causative gene to be the homolog of Arabidopsis High Fluorescence (HCF244) gene, or CrHCF244. We then demonstrated that CrHCF244 is required for psbA translation in the alga, consistent with the function of HCF244 in Arabidopsis. The Arabidopsis HCF244 gene also partially complemented the algal mutant. These results experimentally support the functional conservation of the homologs in green algae and land plants. Intriguingly, the CrHCF244 mutant also exhibited a relatively high rate of suppressor mutants, pointing to the presence of alternative factor(s)/pathway(s) for D1 translation control. The establishment of CrHCF244 as a psbA translation factor in Chlamydomonas showed the similarities in psbA translation regulation in algae and plants. The future identification of the alternative factor(s) in this alga will provide insights on psbA translation in plants. HighlightWe identified CrHCF244 as a translation factor of psbA in Chlamydomonas. Arabidopsis HCF244 partially complements Chlamydomonas {Delta}CrHCF244 mutant, indicating semi-conservation of the function of this gene between organisms. Suppressor mutants of {Delta}CrHCF244 suggest the presence of alternative translation factors in psbA translation.

plant biology↗