Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 1,279 records · Page 71Linked to original sources

bioRxiv2020

LACCASE is Necessary for Root Development in Salvia miltiorrhiza

Laccases are multicopper-containing glycoproteins related to monolignol oxidation and polymerization. These properties indicate that laccases are involved in the formation of important medicinal phenolic acid compounds in Salvia miltiorrhiza such as salvianolic acid B (SAB), which is used for cardiovascular disease treatment. To date, 29 laccases have been found in S. miltiorrhiza, some of which influence the synthesis of phenolic acids. Because of the functional redundancy of laccase genes, their roles in S. miltiorrhiza are poorly understood. In this study, the CRISPR/Cas9 system was first used for dual gene locus targeting in S. miltiorrhiza to knock out multiple laccase family genes. The development of the roots was retarded, and root microstructure was abnormal in laccase mutant lines. Additionally, the accumulation of phenolic acid compounds as well as lignin was dramatically reduced. This study suggests that SmLACs are necessary for root development and phenolic acid compound metabolism in S. miltiorrhiza.

plant biology↗

bioRxiv2020

New Genes in Drosophila Quickly Evolved Essential Functions in Viability During Development

It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the analyses of gene effects and improvements in the computational identification of new genes, which has led to large sample sizes of new genes, open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including the dating of gene ages, the interpretation of RNAi data that may confuse false positive/false negative rates, and the potential confounding impact of compensation and developmental effects that were not considered during previous CRISPR knockout experiments. We further analyzed new data from knockdowns of 702 new genes (~66% of total 1,070 Drosophila melanogaster new genes), revealing a similarly high proportion of essential genes from recent evolution, compared to those found in distant ancestors of D. melanogaster. Knockout of a few young genes detected analogous essentiality. Furthermore, our experimentally determined distribution and comparison of knockdown efficiency in different RNAi libraries provided valuable data for general functional analyses of genes. Taken together, these data, along with an improved understanding of the phenotypic effect analyses of new genes, provide further evidence to the conclusion that new genes in Drosophila quickly evolved essential functions in viability during development.

developmental biology↗

bioRxiv2020

Microglial synaptic pruning on axon initial segment of dentate granule cells: sexually dimorphic effects on fear response of adult rats subjected to early life stress

Axon initial segments (AIS) of dentate granule cells (GC) in hippocampus exhibit prominent spines during early development that are associated with microglial contacts. Here, we asked if developmental changes in axon initial segment spines (AISS) could be modified by neonatal maternal separation through stress hormones and microglial activation and examined the potential behavioral consequences. We examined AISS densities at postnatal day (PND) 15 and 50, using Golgi-Cox staining and anatomical analysis. Neuron-microglial interaction was assessed using antibodies against ankyrinG, PSD95 and Iba1, for AIS, AISS and microglia, respectively, in normally reared and neonatal maternally separated (MS) male and female rats. We observed a higher density of AISS in MS groups at both PND15 and PND50 compared to control. Effects were more pronounced in female than in male rats. AIS-associated microglia showed a hyper-ramified morphology and less co-localization with PSD95 in MS compared to normally reared animals at PND 15. An MS-like alteration in microglial morphology and synaptic pruning could be produced ex vivo by vasopressin application in acute hippocampal slices from normally reared animals. MS rats exhibited increased freezing behavior during auditory fear memory testing which, like effects on AISS density, was more pronounced in females than males. Freezing behavior was associated with Fos expression in dorsal and ventral dentate GC. In summary, AIS associated microglial activity is altered by MS. Sex differences in the long-term effects of MS on AISS density are penetrant to a behavioral phenotype of increased stimulus reactivity in adult female subjects.

neuroscience↗

bioRxiv2020

Pathogenic measles viruses cannot evolve to bypass vaccine-induced neutralizing antibodies

After centuries of pestilence and decades of global vaccination, measles serotypes capable of evading vaccine-induced immunity have not emerged. Here, by systematically building mutations into the H-glycoprotein of an attenuated measles strain and assaying for serum neutralization, we show that virus evolution is severely constrained by the existence of numerous codominant H-glycoprotein antigenic sites, some critical for binding to pathogenicity receptors SLAMF1 and Nectin-4. We further demonstrate the existence in serum of protective neutralizing antibodies targeting codominant F-glycoprotein epitopes. Calculations suggest that evolution of pathogenic measles viruses capable of escaping serum neutralization in vaccinated individuals is a near-zero probability scenario.

microbiology↗

bioRxiv2020

Spatial and Temporal Organization of Odor-evoked Responses in a Fly Olfactory Circuit: Inputs, Outputs and Idiosyncrasies

How is sensory information routed through different types of neurons within a circuit, and do equivalent circuits in different individuals follow similar organizational principles? We examined this issue in the fruit fly olfactory system. Odor-evoked signals from sensory neurons (ORNs) triggered neural responses that were patterned over space and time in cholinergic ePNs and GABAergic iPNs within the antennal lobe. The dendritic-axonal (I/O) response mapping was complex and diverse, and axonal organization was region-specific (mushroom body vs. lateral horn). In the lateral horn, feed-forward excitatory and inhibitory axonal projections matched odor tuning in a stereotyped, dorsal-lateral locus, but mismatched in most other locations. In the temporal dimension, ORN, ePN and iPN odor-evoked responses had similar encoding features, such as information refinement over time and divergent ON and OFF responses. Notably, analogous spatial and temporal coding principles were observed in all flies, and the latter emerged from idiosyncratic neural processing approaches. HighlightsO_LIConsistency and idiosyncrasy both exist in ORN, ePN and iPN functional maps C_LIO_LISignal transformations between different ePN compartments are complex and diverse C_LIO_LITemporal decorrelation between stimuli happens in all three neuronal populations C_LIO_LIOFF responses that are orthogonal to ON responses emerge after odor termination C_LI

neuroscience↗

bioRxiv2020

Systematic characterization and genetic interaction analysis of adhesins in Candida albicans virulence

Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of the role and relationships between these adhesins has not been explored. We previously established a CRISPR-based platform for efficient generation of single- and double-gene deletions in C. albicans, which was used to construct a library of 144 mutants, comprising 12 unique adhesin genes deleted singly, or in every possible combination of double deletions. Here, we exploit this adhesin mutant library to explore the role of adhesin proteins in C. albicans virulence. We perform a comprehensive, high-throughput screen of this library, using Caenorhabditis elegans as a simplified model host system, which identified mutants critical for virulence and significant genetic interactions. We perform follow-up analysis to assess the ability of high- and low-virulence strains to undergo cellular morphogenesis and form biofilms in vitro, as well as to colonize the C. elegans host. We further perform genetic interaction analysis to identify novel significant negative genetic interactions between adhesin mutants, whereby combinatorial perturbation of these genes significantly impairs virulence, more than expected based on virulence of the single mutant constituent strains. Together, this yields important new insight into the role of adhesins, singly and in combinations, in mediating diverse facets of virulence of this critical fungal pathogen. SummaryCandida albicans is a human fungal pathogen and cause of life-threatening systemic infections. Cell surface-associated adhesins play a central role in this pathogens ability to establish infection. Here, we provide a comprehensive analysis of adhesin factors, and their role in fungal virulence. Exploiting a high-throughput workflow, we screened an adhesin mutant library using C. elegans as a simple model host, and identified mutants and genetic interactions involved in virulence. We found that adhesin mutants are impaired in in vitro pathogenicity, irrespective of their virulence. Together, this work provides new insight into the role of adhesin factors in mediating fungal virulence.

microbiology↗

bioRxiv2020

Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization

Sperm cooperation has been observed in multiple species, yet its existence and benefit for reproductive success in mammals remains underexplored. Here, combining tissue-clearing with deep three-dimensional imaging, we demonstrate that postcopulatory mouse sperm congregate into unidirectional sperm cooperative clusters at the utero-tubal junction (UTJ), a key physical barrier for passage into the oviduct. Reducing sperm number in male mice by unilateral vasoligation or busulfan-treatment impairs sperm cluster formation and oviduct entry. Interestingly, sperm derived from Tex101-/- mouse has normal number, motility and morphology, yet they cannot form sperm cluster and fail to pass through the UTJ, which is at least in part due to the altered tail beating pattern of the Tex101-/- sperm. Moreover, Tex101-/- sperms defect in oviduct entry cannot be rescued by the presence of wild-type (WT) sperm in the same uteri by sequential mating, suggesting sperm cooperative cluster as an essential behavior contributing to male fertility, which could be related to human infertility or subfertility.

developmental biology↗

bioRxiv2020

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs

MotivationDue to the complexity of metagenomic community, de novo assembly on next generation sequencing data is commonly unable to produce microbial complete genomes. Metagenomic binning is a crucial task that could group the fragmented contigs into clusters based on their nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Assembly and paired-end graphs can provide the connectedness between contigs, where the linked contigs have high chance to be derived from the same clusters. ResultsWe developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and paired-end graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends subgraphs. METAMVGL could learn the graphs weights automatically and predict the contig labels in a uniform multi-view label propagation framework. In the experiments, we observed METAMVGL significantly increased the high-confident edges in the combined graph and linked dead ends to the main graph. It also outperformed with many state-of-the-art binning methods, MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and Graphbin on the metagenomic sequencing from simulation, two mock communities and real Sharon data. Availability and implementationThe software is available at https://github.com/ZhangZhenmiao/METAMVGL.

bioinformatics↗

bioRxiv2020

A novel viral protein translation mechanism reveals mitochondria as a target for antiviral drug development

The ongoing Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic has acutely highlighted the need to identify new treatment strategies for viral infections. Here we present a pivotal molecular mechanism of viral protein translation that relies on the mitochondrial translation machinery. We found that rare codons such as Leu-TTA are highly enriched in many viruses, including SARS-CoV-2, and these codons are essential for the regulation of viral protein expression. SARS-CoV-2 controls the translation of its spike gene by hijacking host mitochondria through 5 leader and 3UTR sequences that contain mitochondrial localization signals and activate the EGR1 pathway. Mitochondrial-targeted drugs such as lonidamine and polydatin significantly repress rare codon-driven gene expression and viral replication. This study identifies an unreported viral protein translation mechanism and opens up a novel avenue for developing antiviral drugs. One Sentence SummaryMitochondria are a potential target for antiviral therapy

microbiology↗

bioRxiv2020

Photochemical probe identification of the small-molecule binding site in a mammalian membrane-bound O-acyltransferase

The mammalian membrane-bound O-acyltransferase (MBOAT) superfamily is involved in biological processes including growth, development and appetite sensing. MBOATs are attractive drug targets in cancer and obesity; however, information on the binding site and molecular mechanisms underlying small-molecule inhibition is elusive. This study reports development of a photochemical probe to interrogate the small-molecule binding site in the human MBOAT Hedgehog acyltransferase (HHAT) based on HHAT inhibitor RUSKI-201. Structure-activity relationship investigation identified the improved enantiomeric inhibitor IMP-1575, which is the most potent HHAT inhibitor reported to-date, and guided rational design of a photocrosslinking probe that maintained HHAT-inhibitory potency. Photocrosslinking and proteomic sequencing of HHAT delivered identification of the first small-molecule binding site in a mammalian MBOAT. Topology and homology data suggested a potential mechanism for HHAT inhibition which was confirmed via kinetic analysis. Our results provide an optimal HHAT inhibitor IMP-1575 (Ki = 38 nM) and a strategy for mapping of interaction sites in MBOATs.

biochemistry↗

bioRxiv2020

CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA

Proper expressions of Homeobox A cluster genes (HoxA) are essential for embryonic stem cells (ESC) differentiation and individual development. However, the mechanisms underlying controlling precise spatiotemporal expressions of HoxA during early ESC differentiation remain poorly understood. Herein, we identified a functional CTCF-binding element (CBE+47) closest to the 3-end of HoxA within the same topologically associated domain (TAD) in ESC. CRISPR-Cas9 mediated the CBE+47 deletion significantly promotes retinoic acid (RA)-induced HoxA expression and early ESC abnormal differentiation. In delineating its underlying mechanisms, we find that CBE+47 can precisely organize chromatin interactions between its adjacent enhancers and HoxA by using chromosome conformation capture assay (Capture-C). Furthermore, we also find that its adjacent enhancers as enhancer-enhancer interaction complex (EEIC) are required for RA-induced HoxA activation. Collectively, these results provide a new insight for RA-induced HoxA expression, also highlight the unique and precise regulatory roles of CBE in ESC differentiation.

developmental biology↗

bioRxiv2020

Arachidonic acid metabolism controls macrophage alternative activation through regulating oxidative phosphorylation in PPARG dependent manner

Macrophages polarization is mainly controlled by metabolic reprogramming in microenvironment, thus leading to distinct outcomes of various diseases. However, the role of lipid metabolism in the regulation of macrophage alternative activation is incompletely understood. Using human THP-1 and mouse bone marrow derived macrophages polarization models, we revealed a pivotal role for arachidonic acid metabolism in controlling the polarization of M1 and M2 macrophages. We demonstrated that M2 macrophage polarization was inhibited by arachidonic acid, but inversely facilitated by its derived metabolite prostaglandin E2 (PGE2). Furthermore, PPARG bridges these two unconnected processes via modulating oxidative phosphorylation. These results highlight the critical role of arachidonic acid metabolism as an immune regulator in modulating metabolic homeostasis and pathological process.

immunology↗

bioRxiv2020

Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis

Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a new mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5) and We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.

plant biology↗

bioRxiv2020

Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies

Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus virus diseases 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2 infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). In order to understand the mechanism of these nAbs on neutralizing SARS-CoV-2 virus infections, we have performed cryo-EM analysis and here report cryo-EM structures of the ten most potent nAbs in their native full-length IgG or Fab forms bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBD in the "up" conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and their correlation with more potent neutralization and the shedding of S1 subunit.

microbiology↗

bioRxiv2020

Tropomyosin in mugwort cross-reacts to house dust mite, eliciting non-Th2 response in allergic rhinitis patients sensitized to house dust mite

BackgroundMugwort and house dust mite (HDM) are two of the most common inhalant allergens in Asia; however, whether or not mugwort affects polysensitized HDM+ allergic rhinitis (AR) patients has not been elucidated. MethodsOverall, 15884 AR outpatients were assessed for clinical status. Amino acid sequences of mugwort were determined by mass spectrometry. Afterward, cross-reactivity between mugwort tropomyosin and Dermatophagoides pteronyssinus 10 (Der p10) was analysed by ELISA inhibition and basophils activation experiments. To compare immunologic responses eliciting by two different tropomyosins, peripheral blood mononuclear cells (PBMCs) of HDM-monosensitized patients were stimulated by mugwort, HDM, Der p10 and synthetic peptides representing mugwort tropomyosin respectively. ResultsPolysensitized HDM+AR patients were mainly sensitized to cat and mugwort, and the positive rate of monosensitized HDM+AR out-clinic patients was increased during the mugwort pollen season. Mugwort tropomyosin protein had similar structural domains to HDM tropomyosin, Der p10. ELISA inhibition experiment showed synthetic mugwort tropomyosin peptide inhibited IgE binding to Der p10; mugwort tropomyosin peptide activated basophils which were primed by HDM-specific IgE. Unlike HDM and Derp 10, mugwort and mugwort tropomyosin mainly induced IFN-{gamma} and IL-17, release in PBMCs of monosensitized HDM+AR patients, but not IL-5. ConclusionsPan-allergen tropomyosin is a major protein accounting for the cross-reactivity between mugwort and HDM, which reminds HDM+ patients to reduce mugwort exposure in mugwort pollen season in virtue of the tropomyosin induced mild inflammation.

immunology↗

bioRxiv2020

TRAF4 inhibits bladder cancer progression by promoting BMP/SMAD signalling pathway

Bladder cancer is one of the most prevalent cancer types in the world, frequently exhibiting invasion and metastasis and therefore associated with poor prognosis. It is a progressive disease with high recurrence rates even after surgery, which calls for the urgent need for early intervention and diagnosis. The E3 ubiquitin ligase TNF Receptor Associated Factor 4 (TRAF4) has been largely implicated as a tumour-promoting element in a wide range of cancers. Over-expression and amplification of this gene product has been a common observation in breast and other metastatic tumours. In contrast, we observed that expression of TRAF4 negatively correlated with overall patient survival. Moreover, its expression was repressed at epigenetic levels in aggressive bladder cancer cells. We also describe an ERK kinase phosphorylation site on TRAF4 that inhibits its stability and localization to plasma membrane in such cells. Furthermore, knockdown of TRAF4 in epithelial bladder cancer cell lines leads to gain of mesenchymal genes and a loss of epithelial integrity. Reciprocally, stable over-expression of TRAF4 in mesenchymal cells leads to decreased migratory and invasive properties. Transcriptomic analysis upon TRAF4 mis-expression in bladder cancer cell lines revealed that higher TRAF4 expression enhanced BMP/SMAD and dampened NF-{kappa}B signalling pathways. Importantly, this notion was confirmed in bladder cancer patient material. Mechanistically, we showed that TRAF4 targets the E3 ubiquitin ligase SMURF1, a negative regulator of BMP/SMAD signalling, for proteasomal degradation in bladder cancer cells. We show that genetic and pharmacological inhibition of SMURF1 or its function inhibited migration of aggressive (mesenchymal) bladder cancer cells.

cancer biology↗

bioRxiv2020

A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG

The cell wall is a stress-bearing structure and a unifying trait in bacteria. Without exception, synthesis of the cell wall involves formation of the precursor molecule Lipid II by the activity of the essential biosynthetic enzyme MurG, which is encoded in the division and cell wall synthesis (dcw) gene cluster. Here we present the discovery of a novel cell wall enzyme that can substitute for MurG. A mutant of Kitasatospora viridifaciens lacking a significant part of the dcw cluster including murG surprisingly produced Lipid II and wild-type peptidoglycan. Genomic analysis identified a distant murG paralogue, which encodes a putative enzyme that shares only around 31% aa sequence identity with MurG. We show that this enzyme can replace the canonical MurG, and we therefore designated it MurG2. Orthologues of murG2 are present in 38% of all genomes of Kitasatosporae and members of the sister genus Streptomyces. CRISPRi experiments showed that K. viridifaciens murG2 can also functionally replace murG in Streptomyces coelicolor, thus validating its bioactivity and demonstrating that it is active in multiple genera. Altogether, these results identify MurG2 as a bona fide Lipid II synthase, thus demonstrating plasticity in cell wall synthesis.

microbiology↗

bioRxiv2020

Fast-Bonito: A Faster Basecaller for Nanopore Sequencing

Oxford Nanopore Technologies (ONT) is a promising sequencing technology that could generate relatively longer sequencing reads compared to the next generation sequencing (NGS) technology. The base calling process is very important for TGS. It translates the original electrical signals from the sequencer to the nucleotide sequence. By doing that, the base calling could significantly influence the accuracy of downstream analysis. Bonito is a recently developed basecaller based on deep neuron network, the neuron network architecture of which is composed of a single convolutional layer followed by three stacked bidirectional GRU layers. Although Bonito achieved the state-of-the-art accuracy, its speed is so slow that it is not likely to be used in production. We therefore implement Fast-Bonito, which introduces systematic optimization to speed up Bonito. Fast-Bonito archives 53.8% faster than the original version on NVIDIA V100 and could be further speed up by HUAWEI Ascend 910 NPU, achieving 565% faster than the original version. The accuracy of Fast-Bonito is also slightly higher than the original Bonito.

bioinformatics↗