Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

At least 217 records · Page 12Linked to original sources

bioRxiv2020

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification

Brassica oleracea includes several morphologically diverse, economically important vegetable crops. Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~120 K high-confidence structural variants (SVs). Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

plant biology↗

bioRxiv2020

RBM20 phosphorylation on serine/arginine domain is crucial to regulate pre-mRNA splicing and protein shuttling in the heart

Molecular and cellular mechanisms of mutations of splicing factors in heart function are not well understood. The splicing of precursor mRNA is dependent on an essential group of splicing factors containing serine-arginine (SR) domain(s) that are critical for protein-RNA and protein-protein interaction in the spliceosome assembly. Phosphorylation of SR domains plays a key role in splicing control and the distribution of splicing factors in the cell. RNA binding motif 20 (RBM20) is a splicing factor predominantly expressed in muscle tissues with the highest expression level in the heart. However, its phosphorylation status is completely unknown up-to-date. In this study, we identified sixteen amino acid residues that are phosphorylated by middle-down mass spectrometry. Four of them are located in the SR domain, and two out of the four residues, S638 and S640, play an essential role in splicing control and facilitate RBM20 shuttling from the nucleus to the cytoplasm. Re-localization of RBM20 promotes protein aggregation in the cytoplasm. We have also verified that SR-protein kinases (SRPKs), cdc2-like kinases (CLKs) and protein kinase B (PKB or AKT) phosphorylate S638 and S640. Mutations of S638A and S640G reduce RBM20 phosphorylation and disrupt the splicing. Taken together, we determine the phosphorylation status of RBM20 and provide the first evidence that phosphorylation on SR domain is crucial for pre-mRNA splicing and protein trafficking. Our findings reveal a new role of RBM20 via protein shuttling in cardiac function.

cell biology↗

bioRxiv2020

Discordant transcriptional signatures of mitochondrial genes in Parkinson's disease human myeloid cells

An increasing number of identified Parkinsons disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their potential role in pathological mechanisms is not obvious. We have generated transcriptomic profiles of CD14+ monocytes from 230 individuals with sporadic PD and age-matched healthy subjects. We identified dysregulation of genes involved in mitochondrial and proteasomal function. We also generated transcriptomic profiles of primary microglia from autopsied brains of 55 PD and control subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified PD susceptibility genes, whose expression, relative to each risk allele, is altered in monocytes. These findings reveal that transcriptomic mitochondrial alterations are detectable in PD monocytes and are distinct from brain microglia, and facilitates efforts to understand the roles of myeloid cells in PD.

neuroscience↗

bioRxiv2020

Herbivore-induced activation of viral phosphatase disarms plant antiviral immunities for pathogen transmission

The survival of pathogens depends on their ability to overcome host immunity, especially arthropod-borne viruses (arboviruses) which must withstand the immune responses of both the host and the arthropod vector. Successful arboviruses often modify host immunity to accelerate pathogen transmission; however, few studies have explored the underlying mechanism. Here we report attracted herbivore infestation on the virus-infected plants promote transmission by the associated vector herbivore. This herbivore-induced defense suppression underpins a subversive mechanism used by Begomovirus, the largest genus of plant viruses, to compromise host defense for pathogen transmission. Begomovirus-infected plants accumulated {beta}C1 proteins in the phloem where they were bound to host defense regulators, transcription factor WRKY20 and two mitogen-activated protein kinases MPK3 and MPK6. Once perceiving whitefly herbivory or endogenous secreted peptide PEP1, the plants started dephosphorylation on serine33 and stimulated {beta}C1 protein as a phosphatase. {beta}C1 dephosphorylated MPK3/6 and WRKY20, the latter negatively regulated salicylic acid signaling and vascular callose deposition. This viral hijacking of WRKY20 accumulated more vascular callose by which enforced whitefly prolonged salivation and phloem sap ingestion, therefore impelling more virus transmission among plants. We present a scenario in which viruses dynamically respond to the presence of their vectors, suppressing host immunity and promoting pathogen transmission only when needed.

microbiology↗

bioRxiv2020

Tyrosine kinase inhibitors induce mitochondrial dysfunction during cardiomyocyte differentiation through alteration of GATA4-mediated networks

Maternal drug exposure during pregnancy increases the risks of developmental cardiotoxicity, leading to congenital heart defects (CHDs). In this study, we used human stem cells as an in-vitro system to interrogate the mechanisms underlying drug-induced toxicity during cardiomyocyte differentiation, including anticancer tyrosine kinase inhibitor (TKI) drugs (imatinib, sunitinib, and vandetanib). H1-ESCs were treated with these drugs at sublethal levels during cardiomyocyte differentiation. We found that early exposure to TKIs during differentiation induced obvious toxic effects in differentiated cardiomyocytes, including disarranged sarcomere structure, interrupted Ca2+-handling, and impaired mitochondrial function. As sunitinib exposure showed the most significant developmental cardiotoxicity of all TKIs, we further examine its effect with in-vivo experiments. Maternal sunitinib exposure caused fetal death, bioaccumulation, and histopathologic changes in the neonatal mice. Integrative analysis of both transcriptomic and chromatin accessibility landscapes revealed that TKI-exposure altered GATA4-mediated regulatory network, which included key mitochondrial genes. Overexpression of GATA4 with CRISPR-activation restored morphologies, contraction, and mitochondria function in cardiomyocytes upon TKI exposure early during differentiation. Altogether, our study identified a novel crosstalk mechanism between GATA4 activity and mitochondrial function during cardiomyocyte differentiation, and revealed potential therapeutic approaches for reducing TKI-induced developmental cardiotoxicity for human health. HighlightsO_LIEarly-stage exposure to TKIs induced cardiotoxicity and mitochondrial dysfunction C_LIO_LIGATA4 transcriptional activity is inhibited by TKIs C_LIO_LINetwork analysis reveals interactions between GATA4 and mitochondrial genes C_LIO_LIGATA4-overexpression rescues cardiomyocytes and mitochondria from TKI exposure C_LI

systems biology↗

bioRxiv2020

DCP, First Generation PET Radiotracer for Diagnosis of Radiation Resistant Head and Neck Cancer

Redox metabolism plays essential functions in the pathology of cancer. As tumor redox profiles uniquely reflect cancer stage and in select cases, therapeutic sensitivity, the capability to image redox molecular features is essential to improve diagnosis, treatment, and overall quality-of-life (QOL) of cancer patients. While a number of radiotracers for imaging redox metabolism have been developed, there are no reports of radiotracers for in vivo imaging of protein oxidation. Here we take the first step towards this goal and describe the synthesis and kinetic properties of a new positron emission tomography (PET) [18F]DCP radiotracer for in vivo imaging of protein sulfenylation. Time course biodistribution and PET/CT studies using xenograft animal models of Head and Neck Squamous Cell Cancer (HNSCC) demonstrate feasibility of diagnosing radiation resistant tumors, which display lower [18F]DCP signal. These findings are consistent with our previous reports of decreased protein sulfenylation in clinical specimens of radiation resistant HNSCC. We anticipate further development and implementation of this concept in clinical practice to improve the diagnosis of patients with radiation resistant tumors and the accuracy of prognosis for patients undergoing radiation treatment. Single Sentence SummaryThe study introduces a new PET radiotracer for profiling tumor protein oxidation as a prognostic indicator of resistance to radiation therapy.

cancer biology↗

bioRxiv2020

Structural basis for the inhibition of COVID-19 virus main protease by carmofur, an antineoplastic drug

The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease (Mpro). Here the X-ray crystal structure of Mpro in complex with Carmofur reveals that the carbonyl reactive group of Carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 M) and it is a promising lead compound to develop new antiviral treatment for COVID-19.

biochemistry↗

bioRxiv2020

Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit

Some crops inhibit shoot growth but maintain root growth under water-deficit conditions. Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants remains a major challenge. We developed an efficient platform for identifying core transcription factors (TFs) that collectively regulate each other and/or themselves in response to water stress, and exploring their interconnected regulatory circuitry involved in root growth maintenance under water deficit in soybean. We performed multi-species phylogenetic footprinting combined with spatial-temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to identify conserved motifs that function in the water-stress response. Using these functional conserved cis-motifs, we applied a new approach to trace back motifs-associated core TFs ingroup as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We integrated a co-functional TF-TF network and conserved motif-centered TF-DNA networks to construct a core TF network defined by mutual cross-regulation among core TFs. We found that core TF ARG (Abscisic acid response element binding factor-like Root Growth regulator) represses BRG (Brassinosteroid enhanced expression-like Root Growth regulator) expression through binding to its promoter at a conserved binding site. ARG and BRG antagonistically regulate Phytochrome-interacting factor-like Root Growth regulator (PRG) and combinatorially regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light and multiple hormone signaling pathways and maintain root growth in response to varying degrees of water stress. Our study provides valuable information to unravel the complicated mechanisms of molecular networks involved in the regulation of root growth under water deficit.

plant biology↗

bioRxiv2020

Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target

A novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-[A]. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified {beta}-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp. One Sentence SummaryStructure of 2019-nCov RNA polymerase.

biochemistry↗

bioRxiv2020

Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors

Identifying significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose, but they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors, which can result in inaccurate estimations. We propose a computational model, k-Lognormal-Dirichlet-Multinomial model (kLDM), which estimates multiple association networks that correspond to specific environmental conditions according to values of environmental factors (EFs), and simultaneously infers microbe-microbe and environmental factor-microbe associations for each network. We showed the effectiveness of kLDM on synthetic data, a colorectal cancer dataset, as well as the TARA Oceans and American Gut project datasets. The results showed that the widely used Spearmans rank correlation coefficient (SCC) performed much worse than other methods, indicating the importance of separating samples by environmental conditions. We compared cancer fecal samples with cancer-free samples, and our estimation showed fewer associations among microbes but stronger associations between specific bacteria such as five colorectal cancer (CRC)-associated OTUs, indicating gut microbe translocation in cancer patients. Some environmental-factor-dependent associations were found within marine eukaryotic community, and gut microbial heterogeneity of irritable bowel disease (IBD) patients was detected. Results demonstrated that kLDM could successfully unravel the underlying biological associations. In summary, our study presents a computational framework that can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and python scripts, together with all experimental datasets are all accessible at Github (https://github.com/tinglab/kLDM.git).

bioinformatics↗

bioRxiv2020

Structural basis of transcription-translation coupling and collision in bacteria.

Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The pioneering ribosome potentially contacts RNA polymerase (RNAP), forming a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here we present a series of structures representing uncoupled, coupled and collided expressome states determined by electron cryomicroscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, stabilizing an otherwise variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance-channel to the RNAP exit-channel. In this collided complex, NusG-linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study. One Sentence SummaryStructures of the molecular assembly executing gene expression shed light on transcription translation coupling.

biochemistry↗

bioRxiv2020

Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds

Microbes active in extremely cold environments are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of twenty snow samples collected during early and late spring in Svalbard, Norway using our computational read-based microbiome function annotation tool, mi-faser. Our results revealed a more diverse microbiome functional capacity and activity in the early compared to in the late spring samples. The dissimilarity between the metagenomes and metatranscriptomes of the same samples was also significantly higher in the early spring. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant organisms, while late spring samples reflect a new community that is metabolically active. We additionally showed that the abundance of the sequencing reads mapping to the fatty acid synthesis-related microbial pathways was significantly positively correlated with organic acid levels, in both our late spring metagenomes and metatranscriptomes. Moreover, the geraniol degradation pathway and the styrene degradation pathway read abundances correlated and inversely correlated, respectively, with the organic acid levels. These results suggest a possible nutrient switch. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.

bioinformatics↗

bioRxiv2020

Protective anti-prion antibodies in human immunoglobulin repertoires

Prion immunotherapy may hold great potential, but antibodies against certain PrP epitopes can be neurotoxic. Here we identified >6000 PrP-binding antibodies in a synthetic human Fab phage display library, 49 of which we characterized in detail. Antibodies directed against the flexible tail of PrP conferred neuroprotection against infectious prions. We then mined published repertoires of circulating B cells from healthy humans and found antibodies similar to the protective phage-derived antibodies. When expressed recombinantly, these antibodies exhibited anti-PrP reactivity. Furthermore, we surveyed 48718 samples from 37894 hospital patients for the presence of anti-PrP IgGs, and found 21 high-titer individuals. The clinical files of these individuals did not reveal any enrichment of specific pathologies, suggesting that anti-PrP autoimmunity is innocuous. The existence of protective anti-prion antibodies in unbiased human immunological repertoires, combined with the reported lack of such antibodies in carriers of disease-associated PRNP mutations, suggests a link to the low incidence of spontaneous prion diseases in human populations.

neuroscience↗

bioRxiv2020

Transposase assisted tagmentation of RNA/DNA hybrid duplexes

Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of activity of transposase assisted RNA/DNA hybrids co-tagmentation (termed "ATRAC-seq") are comparable to traditional RNA-seq methods in terms of gene number, gene body coverage and gene expression analysis; at the meantime, ATRAC-seq enables a one-tube library construction protocol and hence is more rapid (within 8 h) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.

genomics↗

bioRxiv2020

Alteration of fecal microbial compositions and bacterial taxa in female osteoporotic patients

BackgroundGut microbiota, mainly characterized by fecal bacterial compositions, affects human immune system and pathophysiological development. Our aim was to measure the quantitative differences of fecal bacterial compositions between osteoporotic patients and healthy subjects, and to identify novel bacterial taxa that speculate the incidence of osteoporosis in female. MethodWe recruited 104 female subjects, including 45 osteoporotic individuals and 59 healthy control. Fecal samples were collected for further analysis by 16S rRNA quantitative arrays and bioinformatics analysis. ResultsAnalyses of - and {beta}-diversity demonstrated that the diversity and composition of fecal bacterial compositions were both significant different in osteoporosis group, as compared with healthy group. Multiple bacterial genera were significantly increased (e.g., Roseburia and Bacteroides) or decreased (e.g., Streptococcus and Dorea) in the osteoporotic cases. Furthermore, the osteoporosiscould be efficiently determined by the random forest model based on differential taxa (area under ROC curve = 0.93). ConclusionThere were obvious different fecal microbial characteristics between female osteoporosis and healthy subjects. These findings provided evidence for understanding the host-gut microbiota interplay in female osteoporosis, and supported clinical applications of gut microbiota analysis for female osteoporosis diagnosis

microbiology↗

bioRxiv2019

CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of 26S rRNA

Antisense ribosomal siRNAs (risiRNAs) downregulate pre-rRNAs through the nuclear RNAi pathway in Caenorhabditis elegans. However, the biogenesis and regulation of risiRNAs remain obscure. Previously, we showed that 26S rRNAs are uridylated at the 3-ends by an unknown terminal polyuridylation polymerase before the rRNAs are degraded by a 3 to 5 exoribonuclease SUSI-1(ceDIS3L2). There are three polyuridylation polymerases, CDE-1, PUP-2, and PUP-3, in C. elegans. Here, we found that CDE-1 is specifically involved in suppressing risiRNA production. CDE-1 localizes to perinuclear granules in the germline and uridylates both Argonaute-associated 22G-RNAs and 26S rRNAs at the 3-ends. Immunoprecipitation followed by mass spectrometry (IP-MS) revealed that CDE-1 interacts with SUSI-1(ceDIS3L2). Consistent with those results, both CDE-1 and SUSI-1(ceDIS3L2) are required for the inheritance of RNAi. Therefore, this work identified a rRNA surveillance machinery of rRNAs that couples terminal polyuridylation and degradation.

molecular biology↗

bioRxiv2019

A pentylenetetrazole-induced kindling zebrafish larval model for evoked recurrent seizures

BackgroundTransient pentylenetetrazol (PTZ) treatment on zebrafish larvae has been widely accepted a promising animal model for human epilepsy. However, this model is not ideal due to its acuteness and lack of recurrent seizures, which are the key feature of epilepsy in human disease. It is important to develop a more sensitive zebrafish model for epilepsy with well-controlled, predictable, recurrent seizures.\n\nNew MethodThe new method includes an experimental setup and a treatment protocol. The setup tracks the locomotion activity of up to 48 larvae simultaneously, while a visual stimulus can be presented to each of the 48 animals individually. The protocol treated the larvae through a water bath in 5 mM PTZ while being stimulated with rotating grating stimuli for 1 hour/day from 5 to 7 days postfertilization.\n\nResultsThe setup captured the locomotion activity of zebrafish larvae during visual stimulation. The new protocol generated recurrent responses after flashing lights 4 hours post PTZ treatment. The effects could be suppressed by the anti-epileptic drug valproic acid. The characteristics of the visual stimulus play a major role in this kindling model.\n\nComparisons with Existing MethodsWe compared the proposed method with the transient PTZ model and confirmed that the flashing-light-evoked recurrent seizure is a new feature in addition to the transient changes.\n\nConclusionsThe new method generated non-drug-triggered predictable recurrent seizures in response to intermittent photic stimulation in zebrafish larvae and may serve as a sensitive method for anti-epileptic drug screening or a new research protocol in epilepsy research.

neuroscience↗

bioRxiv2019

FRA1 modulates cortical microtubule localization of CMU proteins

Construction of the cell wall demands harmonized deposition of cellulose and matrix polysaccharides. Cortical microtubules orient the deposition of cellulose by guiding the trajectory of plasma membrane-embedded cellulose synthase complexes. Vesicles containing matrix polysaccharides are thought to be transported by the FRA1 kinesin to facilitate their secretion along cortical microtubules. The cortical microtubule cytoskeleton thus provides a platform to coordinate the delivery of cellulose and matrix polysaccharides, but the underlying molecular mechanisms remain unknown. Here, we show that the tail region of the FRA1 kinesin physically interacts with CMU proteins which are important for the microtubule-dependent guidance of cellulose synthase complexes. Interaction with CMUs did not affect microtubule binding or motility of the FRA1 kinesin but had an opposing effect on the cortical microtubule localization of CMU1 and CMU2 proteins, thus regulating the lateral stability of cortical microtubules. Phosphorylation of the FRA1 tail region by CKL6 inhibited binding to CMUs and consequently reversed the extent of cortical microtubule decoration by CMU1 and CMU2. Genetic experiments demonstrated the significance of this interaction to the growth and reproduction of Arabidopsis thaliana plants. We propose that modulation of CMUs microtubule localization by FRA1 provides a mechanism to control the coordinated deposition of cellulose and matrix polysaccharides.

plant biology↗