Biology subjects

Yang, Z.

Publications and source records attributed to Yang, Z..

At least 217 records · Page 12Linked to original sources

bioRxiv2024

Discovery and Biosynthesis of Nyuzenamides D and E by Genome Mining in Streptomyces hygroscopicus

Nyuzenamides belong to the class of bioactive cinnamoyl moiety containing non-ribosomal peptides (NRPs). However, their biosynthetic gene cluster (BGC) remains unconfirmed. Genome-mining revealed a putative nyu BGC in Streptomyces hygroscopicus DSM 40578. Nyuzenamides D (1) and E (2) were subsequently isolated, and the structures were elucidated by detailed NMR spectroscopic and MS spectrometric data analyses. The absolute configuration of 1 was determined by a single-crystal X-ray diffraction study. Through retro-biosynthesis and CRISPR-genome editing, the non-ribosomal peptide synthetase biosynthetic gene cluster for nyuzenamides was confirmed. Our discovery enriches the diversity of cinnamoyl-containing nonribosomal peptides and validates the biosynthetic gene clusters for future genome-mining research.

microbiology↗

bioRxiv2024

Spatially barcoding biochemical reactions using DNA nanostructures unveil a major contact mechanism in proximity labeling

Proximity labeling techniques like TurboID and APEX2 have become pivotal tools in spatial omics research for studying protein interactions. However, the biochemical mechanisms underlying these reactive species-mediated labelings, particularly the spatial patterns of labeling methods within the sub-m range, remain poorly understood. Here, we employed DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 through in vitro assays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using quantitative PCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits a low-level diffusive labeling towards more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes, at the same time highlight the potential of DNA nanotechnology in spatially profiling reactive species.

biochemistry↗

bioRxiv2024

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, the structure, function, and evolutionary history of the genomic regions associated with this fusion remain poorly understood. Here, we analyze finished telomere-to-telomere chromosomes in great apes and macaques to show that the fusion was associated with multiple pericentric inversions, segmental duplications (SDs), and the rapid turnover of subterminal repetitive DNA. We characterized the fusion site at single-base-pair resolution and identified three distinct SDs that originated more than 5 million years ago. These three distinct SDs were differentially distributed among African great apes as a result of incomplete lineage sorting (ILS) and lineage-specific duplication. Most conspicuously, one of these SDs shares homology to a hypomethylated SD spacer sequence present in hundreds of copies in the subterminal heterochromatin of chimpanzees and bonobos. The fusion in human was accompanied by a systematic degradation of the three divergent -satellite arrays representing the ancestral centromere creating five distinct structural haplotypes in humans. CRISPR/Cas9-mediated depletion of the fusion site in human cell lines significantly alters the expression of 108 genes, indicating a potential regulatory consequence to this human-specific karyotypic change.

evolutionary biology↗

bioRxiv2024

Polyphosphate as a Novel Regulator of Super-Enhancer Complexes: Disruption of Phase Separation and Gene Expression

Inorganic polyphosphate (polyP) is a highly conserved linear polymer of orthophosphate, present across nearly all living organisms. Its functional diversity, particularly through recently discovered post-translational modifications, has garnered increasing scientific interest. However, its role in gene regulation, especially in mammalian systems, remains unexplored. In this study, we present findings that demonstrate that polyP multi-targets the super-enhancer complex to regulate gene expression, marking a novel mechanism of transcriptional control. We show that polyP modifies key components of the complex, including the Mediator subunit MED1, the coactivator Bromodomain-containing protein 4 (BRD4), and the transcriptional regulator Yin Yang 1 (YY1). This polyP-mediated modification not only disrupts their ability to undergo phase separation but also downregulates the expression of MED1 and BRD4, as well as impairs the nuclear localization of YY1. Furthermore, polyP inhibits YY1 dimer formation and disrupts YY1-mediated DNA looping, leading to suppressed gene expression. These discoveries highlight polyP as a novel regulator of super-enhancer-driven gene transcription and provide new insights into the broader role of polyP in epigenetic regulation. This work uncovers a previously unknown layer of gene control, positioning polyP as a critical player in transcriptional regulation through its interaction with transcription factors and coactivators. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/628164v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@10b53b2org.highwire.dtl.DTLVardef@a3dc10org.highwire.dtl.DTLVardef@1c4d72forg.highwire.dtl.DTLVardef@b7378_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPolyP modifies key components of the super-enhancer complex BRD4, MED1 and YY1 by targeting their His-rich, Lys-rich or PASK sequences C_LIO_LIPolyP disrupts phase separation of BRD4, MED1 and YY1 C_LIO_LIPolyP impairs YY1s recruitment of BRD4 and MED1 and disrupts nuclear localization, dimerization, DNA looping and DNA binding to YY1 C_LIO_LIPolyP attenuates gene expression mediated by YY1 and BRD4 C_LI

molecular biology↗

bioRxiv2024

Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases

Spatial transcriptomics (ST) has revolutionized our understanding of tissue architecture, yet constructing comprehensive three-dimensional (3D) cell atlases remains challenging due to technical limitations and high cost. Current approaches typically capture only sparsely sampled two-dimensional sections, leaving substantial gaps that limit our understanding of continuous organ organization. Here, we present SpatialZ, a computational framework that bridges these gaps by generating virtual slices between experimentally measured sections, enabling the construction of dense 3D cell atlases from planar ST data. SpatialZ is designed to operate at single-cell resolution and function independently of gene coverage limitations inherent to specific spatial technologies. Comprehensive validation using real 3D ST and independent serial sectioning datasets demonstrates that SpatialZ accurately reconstructs virtual slices while preserving cell identities, gene expression patterns, and spatial relationships. Leveraging the BRAIN Initiative Cell Census Network data, we constructed a 3D hemisphere atlas comprising over 38 million cells, a scale not feasible experimentally. This dense atlas enables unprecedented capabilities, including in silico sectioning at arbitrary angles, explorations of gene expression across both 3D volumes and surfaces, and 3D mapping of query tissue sections. While currently validated for spatial transcriptomics, the underlying principles of SpatialZ could potentially be adapted for spatial proteomics, spatial metabolomics, and even spatial multi-omics. Validated through internal and external testing, our computationally generated atlas maintains biological accuracy, providing unprecedented resolution of spatial molecular landscapes and demonstrating the potential of computational approaches in advancing 3D ST.

bioinformatics↗

bioRxiv2024

The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plants

Parasitic plants in Orobanchaceae are noxious agricultural pests that severely impact crops worldwide. These plants acquire water and nutrients from their hosts through a specialized organ called the haustorium. A key step in haustorium development involves cell wall modification. In this study, we identified and analyzed the evolutionary relationships of pectate lyase-like (PLL) genes across parasitic plants and other non-parasitic land plant lineages. To support detailed examination of gene models and paralogous gene family members, we used published parasitic plant genomes, as well as a recently generated draft genome assembly and annotation of Triphysaria versicolor. One particular PLL gene, denoted as PLL1 in parasitic Orobanchaceae, emerged as an important candidate gene for parasitism. Our previous comparative transcriptomic analyses showed that PLL1 underwent neofunctionalization via an expression shift from floral tissues in non-parasitic relatives to haustoria in parasitic species. It belongs to the largest sub-clade of the PLL gene family, is highly upregulated in haustoria, and shows signatures of relaxed purifying selection and 15 individual sites with signatures of adaptive evolution. To explore its function in haustorium development, we manipulated PLL1 expression in T. versicolor, a model parasitic species from Orobanchaceae, using direct transformation with the parasite and host-induced-gene-silencing (HIGS). For HIGS, we generated transgenic Medicago hosts expressing hairpin RNAs targeting the PLL1 gene in T. versicolor. An average 60% reduction of PLL1 transcript level was observed in both direct transformation and HIGS treatments, leading to an increased frequency of poorly adhered parasites with fewer xylem connections and a smaller proportion of mature haustoria. These findings demonstrate that PLL1 plays a crucial role in haustorium development and suggest it as a promising target for managing parasitic weeds. Notably, the success of HIGS even before the establishment of a functional haustorium highlights the possibility of early intervention against parasitism.

plant biology↗

bioRxiv2024

Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding

Allosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzymes kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this sites function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2s biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2s role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.

biochemistry↗

bioRxiv2024

The molecular basis of integrated stress response silencing

Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. To counteract this, cells deploy dedicated silencing factors, such as the E3 ligase SIFI that terminates the mitochondrial stress response. How a single enzyme can sense stress across cells and elicit timely stress response inactivation is poorly understood. Here, we report the structure of human SIFI, which revealed how this 1.3MDa complex can target hundreds of proteins for accurate stress response silencing. SIFI attaches the first ubiquitin to substrates using flexible domains within an easily accessible scaffold, yet builds linkage-specific ubiquitin chains at distinct, sterically restricted elongation modules in its periphery. Ubiquitin handover via a ubiquitin-like domain couples versatile substrate modification to precise chain elongation. Stress response silencing therefore exploits a catalytic mechanism that is geared to process many diverse proteins and hence allows a single enzyme to monitor and, if appropriate, modulate a complex cellular state.

biochemistry↗

bioRxiv2024

Optimizing femtosecond laser fabricating strategy of Nitinol hypotube for vascular interventional surgery

Guidewires and catheters are essential in minimally invasive procedures, particularly in accessing targets within the vascular system for neuron surgery. Femtosecond lasers can precisely cut nickel-titanium micro tubes, known as Nitinol hypotubes, serving as the heads of micro guidewires while protecting their core tips. The quality and geometry of these hypotubes depend on the focus of the laser cutting system. We evaluated the cutting efficiency and quality of Nitinol hypotubes using objective lenses with three numerical apertures (NA). Quantitative analysis indicated that higher NA objectives yield better surface quality, resulting in lower debris. Additionally, cutting with high NA objectives produced significantly lower arithmetic mean surface roughness and enhanced mechanical properties. Using a two-temperature model, we simulated the interaction between femtosecond lasers and Nitinol, showing that higher NA objectives increase electron temperatures, thus improving material removal efficiency. This study also tested the optimized Nitinol hypotube prformance in simulations of invasive neuron surgery.

neuroscience↗

bioRxiv2024

Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design

HIV-1 broadly-neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA-class of CD4bs bNAbs includes fewer rare features and somatic hypermutations (SHMs) to achieve broad neutralization, thus presenting a potentially accessible pathway for vaccine-induced bNAb development. Here, we created a library of IOMA variants in which each SHM was individually reverted to the inferred germline (iGL) counterpart to investigate the roles of SHMs in conferring IOMAs neutralization potency and breadth. Impacts on neutralization for each variant were evaluated, and this information was used to design minimally-mutated IOMA-class variants (IOMAmin) that incorporated the fewest SHMs required for achieving IOMAs neutralization breadth. A cryo-EM structure of an IOMAmin variant bound to Env was used to further interpret characteristics of IOMA variants to elucidate how IOMAs structural features correlate with its neutralization mechanism, informing the design of IOMA-targeting immunogens. HighlightsIOMAmin variants with reduced SHMs retain neutralization potency and breadth. Cryo-EM structure reveals IOMAmin preserves key Env interactions despite fewer SHMs. IOMA variants with mutations in CDRH3 and CDRL1 fail to improve neutralization.

immunology↗

bioRxiv2024

R-Spondin Mimetic, SZN-043, Induced Proliferation and Wnt Activity, Two Features Deficient in Human Alcohol-Associated Liver Disease

Liver regeneration is impaired in patients suffering from alcohol-associated liver (ALD) diseases. Wnt ligands and their FZD receptors are dysregulated in diseased livers. R-spondin and their receptors are known to regulate Wnt activity via the stabilization of FZD receptors. Here, we investigated the components of the Wnt and R-Spondin-signaling pathways and their activity in patients with ALD. We found that while hepatocytes retained high levels of differentiation markers such as ASGR1 and ASGR2, the expression of two R-spondin co-receptors, LGR4 and LGR5, and of Wnt target genes, CYP1A2 and others, were strongly reduced. SZN-043, a hepatocyte-targeted R-Spondin mimetic, is a new investigational drug that stimulates the physiological Wnt repair pathway and proliferation of hepatocytes. Here, we show that SZN-043 induced hepatocyte proliferation in all models tested, including humanized mouse livers, a chronic-binge alcohol-induced liver injury, and a CCl4-induced fibrosis mouse model. Altogether, SZN-043 could be beneficial for the treatment of ALD.

pathology↗

bioRxiv2024

Densely Populated Cell and Organelles Segmentation With Multi-Plane Deep Learning Pipeline

The complex and highly intertwined morphology of activated platelets within blood clot thrombi poses significant challenges for segmentation. Here we develop a robust machine vision pipeline for cell and organelle segmentation within volume electron microscope (vEM) datasets and validate that against both model CREMI neuron segmentation challenge data and focused isotropic FIB-SEM imaged platelets and their organelles within a series of ferric chloride indued murine occlusive clots Neural network predictions were collected along multiple planes, capturing 3D correlations using only 2D neural networks. Using a workstation class computer, we segmented and analyzed hundreds of platelets and report quantitative morphological measurements of platelets and their thousands of included organelles. CREMI neuron segmentation challenge analysis produced state-of-the-art outcomes as did platelet data in comparison to manual segmentation. Our work paves the way for large-scale, single cell, 3D studies across multiple examples and lends initial single cell level insights into occlusive thrombus structure and platelet heterogeneity therein. We include a lightweight Jupyter notebook for initializing and running the neural network (Data and Materials Availability). We also provide Amira Avizo protocols for converting neural network outputs to cell and organelle instances and subsequent morphological measurements.

bioengineering↗

bioRxiv2024

Attentional failures after sleep deprivation represent moments of cerebrospinal fluid flow

Sleep deprivation rapidly disrupts cognitive function, and in the long term contributes to neurological disease. Why sleep deprivation has such profound effects on cognition is not well understood. Here, we use simultaneous fast fMRI-EEG to test how sleep deprivation modulates cognitive, neural, and fluid dynamics in the human brain. We demonstrate that after sleep deprivation, sleep-like pulsatile cerebrospinal fluid (CSF) flow events intrude into the awake state. CSF flow is coupled to attentional function, with high flow during attentional impairment. Furthermore, CSF flow is tightly orchestrated in a series of brain-body changes including broadband neuronal shifts, pupil constriction, and altered systemic physiology, pointing to a coupled system of fluid dynamics and neuromodulatory state. The timing of these dynamics is consistent with a vascular mechanism regulated by neuromodulatory state, in which CSF begins to flow outward when attention fails, and flow reverses when attention recovers. The attentional costs of sleep deprivation may thus reflect an irrepressible need for neuronal rest periods and widespread pulsatile fluid flow.

neuroscience↗

bioRxiv2024

Sulfur-species in Zinc-specific Condylar Zones of a Rat Temporomandibular Joint

In this study, we performed synchrotron-based micro-X-ray fluorescence (-XRF) imaging of elements Zn and S, and X-ray absorption near edge spectroscopy (XANES) coupled with -XRF for identification of Zn and S species in the condylar zones of a rat temporomandibular joint (TMJ). Histologic localization of Zn and hypoxia-inducible factor-1 (HIF-1) were mapped using an optical microscope. These data were visually correlated with -XRF and XANES data to provide insights into plausible biological S-species in Z-enriched condylar zones of a rat TMJ. Furthermore, -XRF coupled with micro-X-ray diffraction (-XRD) was used to underline Z-incorporated biological apatite in the subchondral bone and bone of the rat TMJ. Results illustrated the potential dependence between biometal Zn and nonmetal S and their collective governance of cell and tissue functions in a zone-specific manner. Elemental Zn with organic and inorganic S-species at the cartilage-bone interface and transformation of plausible Zn-enriched mineralization kinetics of biological apatite from subchondral bone to condylar bone were ascertained using -XRF-XANES and -XRD. The coupled -XRF-XANES complementing with -XRD and immunohistology provided an informative view of S and Zn and their association with zone-specific biological pathways in situ. Understanding the spatial distributions of the main S-species with redox-inert Zn in regions of cartilage, bone, and the interface is essential for further unlocking questions surrounding formation and resorption-related biomineralization pathways as related to osteoarthritis or genetically inherited diseases. Using these complementary techniques with microspectroscopic spatial information provided insights into the associations between biometal Zn and nonmetal S and a window into detecting the plausible early-stage diagnostic biomarkers for humans with TMJ osteoarthritis.

bioengineering↗

bioRxiv2024

Deep generative model for protein subcellular localization prediction

Protein sequence determines not only its structure but also its subcellular localization. Although a series of artificial intelligence models have been reported to predict protein subcellular localization, most of them provide only textual outputs. Here, we present deepGPS, a deep generative model for protein subcellular localization prediction. After trained with both protein primary sequences and protein subcellular localization fluorescence images, deepGPS shows the ability to predict cytoplasmic and nuclear localizations by reporting both textual labels and generative images as outputs. In addition, deepGPS shows potential to be further extended for other types of subcellular localization prediction, even with limited input data volumes for training. Finally, an openGPS website (https://bits.fudan.edu.cn/opengps) is constructed to provide a public and convenient platform for protein subcellular localization prediction with the scientific community.

bioinformatics↗

bioRxiv2024

A tumor-secreted protein utilizes glucagon release to cause host wasting

Tumor-host interaction plays a critical role in malignant tumor-induced organ wasting across multiple species. Despite known regulation of regional wasting of individual peripheral organs by tumors, whether and how tumors utilize critical host catabolic hormone(s) to simultaneously induce systemic host wasting, however, is largely unknown. Using the conserved yki3SA-tumor model in Drosophila, we discovered that tumors increase the production of adipokinetic hormone (Akh), a glucagon-like catabolic hormone, to cause systemic host wasting, including muscle dysfunction, lipid loss, hyperglycemia, and ovary atrophy. We next integrated RNAi screening and Gal4-LexA dual expression system to identify that yki3SA-gut tumors secrete Pvf1 to remotely activate its receptor Pvr in Akh-producing cells (APCs), ultimately promoting Akh production. The underlying molecular mechanisms involved the Pvf1-Pvr axis that triggers Mmp2-dependent ECM remodeling of APCs and enhances innervation from the excitatory cholinergic neurons. Interestingly, we also confirmed the similar mechanisms governing tumor-induced glucagon release and organ wasting in mammals. Blockade of either glucagon or PDGFR (homolog of Pvr) action efficiently ameliorated organ wasting in the presence of malignant tumors. Therefore, our results demonstrate that tumors remotely promote neural-associated Akh/glucagon production via Pvf1-Pvr axis to cause systemic host wasting.

physiology↗

bioRxiv2024

Dissecting the Heterogeneity and Tumor-Associated Dynamics of Human Liver Group I ILC via scRNA Sequencing Data

Single-cell transcriptome analysis has made outstanding contributions to the identification of new cell lineages and the study of cancer immune microenvironment. Yet, the characterization of human liver ILC1s and their dynamic changes in the tumor microenvironment have not been thoroughly studied at this detailed level. Here, we performed an integrated analysis of mouse and human liver immune cells to identify human liver ILC1 based on identified mouse liver ILC1 and to verify its functional similarity. Additionally, our findings highlighted the different expression patterns of the EOMES gene in human versus mouse group I ILCs, suggesting its reduced regulatory significance in human liver NK cells and ILC1 compared to murine models. A unique subset of CD127hi intermediate ILCs (intILCs) was identified, exhibiting traits of both human liver NK cells and ILC1. Single-cell sequencing data analysis and TCGA were utilized to characterize the distinct alterations in the genes and functions of NK cells, ILC1, and intILCs in human hepatocellular carcinoma. It was found that the dynamic changes of ILC1 and intILCs, along with some of their subpopulations, may be key factors in tumor progression. This study provided new insights into the identification of ILC1 in human liver and the immunologic changes and mechanism of group I ILCs in the tumor microenvironment, and these findings may be applicable to improving the diagnosis and treatment of hepatocellular carcinoma. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/619932v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1976bbeorg.highwire.dtl.DTLVardef@228ce4org.highwire.dtl.DTLVardef@4fcdd4org.highwire.dtl.DTLVardef@1522eff_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Recent codon preference reversals in the Drosophila melanogaster lineage

We employ fine-scale population genetic analyses to reveal dynamics among interacting forces that act at synonymous sites and introns among closely related Drosophila species. Synonymous codon usage bias has proven to be well-suited for population genetic inference. Under major codon preference, translationally superior "major" codons confer fitness benefits relative to their less efficiently and/or accurately decoded synonymous counterparts. Our codon family and lineage-specific analyses expand on previous findings in the Drosophila simulans lineage; patterns in naturally occurring polymorphism demonstrate fixation biases toward GC-ending codons that are consistent in direction, but heterogeneous in magnitude, among synonymous families. These forces are generally stronger than fixation biases in intron sequences. In contrast, population genetic analyses reveal unexpected evidence of codon preference reversals in the Drosophila melanogaster lineage. Codon family-specific polymorphism patterns support reduced efficacy of natural selection in most synonymous families but indicate reversals of favored states in the four codon families encoded by NAY. Accelerated synonymous fixations in favor of NAT and greater differences for both allele frequencies and fixation rates among X-linked, relative to autosomal, loci bolster support for fitness effect reversals. The specificity of preference reversals to codons whose cognate tRNAs undergo wobble position queuosine modification is intriguing. However, our analyses reveal prevalent dinucleotide preferences for ApT over ApC that act in opposition to GC favoring forces in both coding and intron regions. We present evidence that changes in the relative efficacy of translational selection and dinucleotide preference underlie apparent codon preference reversals.

evolutionary biology↗