Biology subjects

Yu, G.

Publications and source records attributed to Yu, G..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Insm1 regulates the development of mTECs and immune tolerance

The Insm1 gene encodes a zinc finger protein with known functions in neuroendocrine cells and neurons. Here we characterized the expression and function of Insm1 in medullary thymic epithelial cells (mTECs). Insm1 is co-expressed with Aire in majority of Insm1 or Aire positive cells, while a few Insm1 positive cells did not express Aire. Mutation of Insm1 impair the expression of Aire and the generation of normal numbers of Aire-expressing mTECs during development. We detected downregulation of genes that expressed specifically in Aire-expressing mTEC and mimetic cells in Insm1 mutant mTECs. Conversely, when Insm1 was overexpressed in thymic epithelial cells in vivo, the size of the mTECs compartment was enlarged and the expression of Aire and genes expressed specifically in the neuroendocrine mimetic cells were increased. Mechanistically, Insm1 bound DNA in mTECs and the majority of the Insm1 binding sites were co-occupied by Aire. These Insm1 binding sites were enriched on super-enhancer regions and thus may contributed to remoted regulation. Both, mice with a thymus-specific mutation in Insm1 or nude mice transplanted with Insm1 mutant thymus, displayed autoimmune responses in multiple peripheral tissues. Together, our data demonstrate a role of Insm1 in development of mTECs and immune tolerance.

immunology↗

bioRxiv2022

Molecular Mechanism for Bacterial Degradation of Plant Hormone Auxin

Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin-degradation (adg) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax adg operon products and identified two proteins, AdgB and AdgI, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that AdgB is a highly IAA-specific ABC transporter solute binding protein, likely involved in IAA uptake. AdgI interacts with AdgH to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene adgJ to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of adgH/I/J genes could enable IAA degradation by E. coli, suggesting a promising strategy for repurposing the adg operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture.

microbiology↗

bioRxiv2022

Alendronate Conjugate for Targeted Delivery to Bone-Forming Prostate Cancer

Bone is the primary metastasis site for lethal prostate cancer, often resulting in poor prognosis, crippling pain, and diminished functioning that drastically reduce both quality of life and survivability. Uniquely, prostate cancer bone metastasis induces aberrant bone overgrowth, due to an increase of osteoblasts induced by tumor-secreted bone morphogenetic protein 4 (BMP4). Conjugating drugs to substances that target the tumor-induced bone area within the metastatic tumor foci would be a promising strategy for drug delivery. To develop such a strategy, we conjugated a near infrared (NIR) fluorescent probe, the dye Cy5.5, to serve as a surrogate for drugs, with alendronate, which targets bone. Characterization, such as infrared spectroscopy, confirmed the synthesis of the Cy5.5-ALN conjugate. The maximum absorbance of free Cy5.5, which was at 675 nm, did not change upon conjugation. Alendronate targeted the bone component hydroxyapatite in a dose-dependent manner up to 2.5 M, with a maximum of 85% of Cy5.5-ALN bound to hydroxyapatite, while free Cy5.5 alone had 6% binding. In in vitro cell binding studies, Cy5.5-ALN bound specifically with mineralized bone matrix of differentiated MC3T3-E1 cells or 2H11 endothelial cells that were induced to become osteoblasts through endothelial-to-osteoblast transition, the underlying mechanism of prostate-cancer-induced bone formation. Neither Cy5.5-ALN nor free Cy5.5 bound to undifferentiated MC3T3-E1 or 2H11 cells. Bone-targeting efficiency studies in non-tumor-bearing mice revealed accumulation over time in the spine, jaw, knees, and paws injected with Cy5.5-ALN, and quantification showed higher accumulation in femurs than in muscle at up to 28 days, while the free Cy5.5 dye was observed circulating without preferential accumulation and decreased over time. There was a linear relationship with fluorescence when the injected concentration of Cy5.5-ALN was between 0.313 and 1.25 nmol/27 g of mouse, as quantified in mouse femurs both in vivo and ex vivo. Ex vivo evaluation of bone-targeting efficiency in nude mice was 3 times higher for bone-forming C4-2b-BMP4 tumors compared to non-bone-forming C4-2b tumors (p-value < 0.001). Fluorescence microscopy imaging of the tumors showed that Cy5.5-ALN co-localized with the bone matrix surrounding tumor-induced bone, but not with the viable tumor cells. Together, these results suggest that a drug-ALN conjugate is a promising approach for targeted delivery of drug to the tumor-induced bone area in the metastatic foci of prostate cancer.

biochemistry↗

bioRxiv2022

Locus-specific proteomics identifies new aspects of the chromatin context involved in V region somatic hypermutation

Activation-induced cytidine deaminase (AID) somatically hypermutates the immunoglobulin heavy chain variable region (IGHV) gene to create the antibody diversity required to resist infections. This hypermutational process involves many pathways including transcription, DNA structural change and repair. While many of the proteins involved have been identified, their relative abundance, organization and regulation have not been resolved and additional factors and pathways need to be identified. To identify the proteome occupying IGHV, we have utilized dCas9-APEX targeted by guide RNAs to biotinylate and enrich the proteins associated with the mutating V region chromatin in the Ramos human B cell line and compared them to the non-mutating downstream constant region (C) chromatin. We identified hundreds of proteins specifically enriched on the V or C region. We confirmed the functionality of selected factors by examining the changes in the V region-specific proteome after inhibiting transcriptional elongation and somatic mutation with the Dot1L inhibitor EPZ004777. SummaryLocus-specific proteomics using dCas9-APEX identifies new aspects of the chromatin context involved in V region somatic hypermutation (SHM) in the human Ramos B cell line. An inhibitor of Dot1L which participates in SHM is used to identify functional SHM-related factors.

immunology↗

bioRxiv2022

Acetylation of a fungal effector that translocates host PR1 facilitates virulence

Pathogens utilize a panoply of effectors to manipulate plant defense. However, despite their importance, relatively little is actually known about regulation of these virulence factors. Here, we show that the effector FolSvp1, secreted from fungal pathogen Fusarium oxysporum f. sp. lycopersici (Fol) directly binds and translocates the tomato pathogenesis-related protein1, SlPR1, from the apoplast outside the plasma membrane to the host nucleus via its nuclear localization signal. Relocation of SlPR1 abolishes generation of the defense signaling peptide, CAPE1, from its C-terminus, and as a consequence, facilitates pathogen invasion of plants. The action of FolSvp1 requires covalent modification by acetylation for full virulence in host tomato tissues. The modification is catalyzed by the Fol FolArd1 lysine acetyltransferase prior to secretion. Addition of an acetyl group to one residue, K167, prevents ubiquitination-dependent degradation of FolSvp1 in both Fol and plant cells with different mechanisms, allowing it to function normally in fungal invasion. Either inactivation of FolSvp1 or removal of the acetyl group on K167 leads to impaired pathogenicity of Fol. These findings indicate that acetylation can regulate the stability of effectors of fungal plant pathogens with impact on virulence.

microbiology↗

bioRxiv2022

Ralstonia solanacearum alters root developmental programs in auxin-dependent and independent manners

Microbial pathogens and other parasites can modify the development of their hosts, either as a target or a side effect of their virulence activities. The plant pathogenic bacterium Ralstonia solanacearum, causal agent of the devastating bacterial wilt disease, is a soil-borne microbe that invades host plants through their roots, and later proliferates in xylem vessels. In this work, we studied the early stages of R. solanacearum infection in the model plant Arabidopsis thaliana, using an in vitro infection system. In addition to the previously reported inhibition of primary root length and increase in root hair formation at the root tip, we observed an earlier xylem differentiation during R. solanacearum infection that occurs in a HrpG-dependent manner, suggesting that the pathogen actively promotes the development of the vascular system upon invasion of the root. Moreover, we found that the phytohormone auxin, of which the accumulation is promoted by the bacterial infection, is required for the R. solanacearum-triggered induction of root hair formation, but not earlier xylem differentiation. Altogether, our results shed light on the capacity of R. solanacearum to induce alterations of root developmental pathways and on the role of auxin in this process.

plant biology↗

bioRxiv2022

Aridity modulates biogeographic distribution and community assembly of cyanobacterial morphotypes in drylands

The patterns of biogeographical distribution and assembly processes of microbiota are of vital importance for understanding ecological adaptation and functioning maintenance that microorganisms provide. Although the assembly of microbial communities was increasingly inspected, the role of their morphological characteristics is still poorly ascertained. Here, by integrating high-throughput sequencing and traditional trait-based classification, we investigated taxonomic and phylogenetic turnovers of different morphotypes of terrestrial cyanobacteria in biocrusts, as a model system, to evaluate the contributions of deterministic and stochastic processes across a large scale in drylands. The results showed that the bundle-forming category dominated in arid ecosystems with high tolerance against environmental fluctuations. Despite strong distance-decay relationships of {beta}-diversity in all categories, both spatial composition and phylogenetic turnover rates of bundle-forming cyanobacteria were significantly lower than unicellular/colonial, heterocystous, and other non-heterocyst filamentous cyanobacteria. Null model analysis of phylogenetic signals and abundance-based neutral model found that stochastic processes prevailed in the assembly, while aridity mediated the balance between determinism and stochasticity and prompted a shifting threshold among morphotypes. Our findings provide a unique perspective to understand the role of microbial morphology, highlighting the differentiation of biogeographic distribution, environmental response, and species preference between morphotypes with consideration of potential functional consequences, and therefore facilitated the prediction of biodiversity loss under climate change.

ecology↗

bioRxiv2022

PvC3H29 interacts with and inhibits DNA binding of PvNAPs to finetune leaf senescence in switchgrass (Panicum virgatum)

Finetuning the progression of leaf senescence is important for plants fitness in nature, while staygreen with delayed leaf senescence has been considered as a valuable agronomic trait in crop genetic improvement. In this study, a switchgrass CCCH-type Zinc finger gene, PvC3H29, was characterized as a suppressor of leaf senescence that over-expressing or suppressing the gene led to delayed or accelerated leaf senescence, respectively. Transcriptomic analysis marked that chlorophyll catabolic pathway genes were involved in the PvC3H29-regulated leaf senescence. PvC3H29 was a nucleus-localized protein with no transcriptional activity. By Y2H screening, we identified its interacting proteins, including a pair of paralogous transcription factors, PvNAP1&2. Over-expressing the PvNAPs led to precocious leaf senescence at least partially by directly targeting and transactivating chlorophyll catabolic genes to promote chlorophyll degradation. PvC3H29, through protein-protein interaction, repressed the DNA-binding efficiency of PvNAPs and alleviated its transactivating effect on downstream genes, thereby functioned as a brake in the progression of leaf senescence. Moreover, over-expressing PvC3H29 resulted in up to 47% higher biomass yield and improved biomass feedstock quality, reiterating the importance of leaf senescence regulation in the genetic improvement of switchgrass and other feedstock crops. One-sentence summaryPvC3H29 interacts with transcription factors, PvNAP1&2, to inhibit their transactivation on chlorophyll catabolism and leaf senescence in switchgrass.

plant biology↗

bioRxiv2022

Structural insights into the viral proteins binding by TRIM7 reveal a general C-terminal glutamine recognition mechanism

The E3 ligase TRIM7 has emerged as a critical player in viral infection and pathogenesis. A recent study found that TRIM7 inhibits human enteroviruses through ubiquitination and proteasomal degradation of viral 2BC protein by targeting the 2C moiety of 2BC protein. Here, we report the crystal structures of TRIM7 in complex with 2C, where the C-terminal region of 2C is inserted into a positively charged groove of the TRIM7 PRY-SPRY domain. Structure-guided biochemical studies revealed the C-terminus glutamine residue of 2C as the primary determinant for TRIM7 binding. Such a glutamine-end motif binding mechanism can be successfully extended to other substrates of TRIM7. More importantly, leveraged by this finding, we were able to identify norovirus and SARS-CoV-2 proteins, and physiological proteins, as new TRIM7 substrates. We further show that TRIM7 may function as a restriction factor to promote the degradation of the viral proteins of norovirus and SARS-CoV-2, thereby restoring the Type I interferon immune response and inhibiting viral infection. Several crystal structures of TRIM7 in complex with SARS-CoV-2 proteins are also determined, and a conserved C-terminus glutamine-specific interaction is observed. These findings unveil a common recognition mode by TRIM7, providing the foundation for further mechanistic characterization of antiviral and cellular functions of TRIM7.

biochemistry↗

bioRxiv2022

Odysseia: Genetic Regulatory Feature Analysis with Interpretable Classification Machine Learning Models

As rapid progress in sequencing technology since last decade, numerous mechanisms underlying cell functions and developmental processes have been revealed as complex regulations of gene expressions. Since single-cell RNA sequencing (scRNA-seq) made high-resolution transcriptomic view increasingly accessible, precise identification of gene regulatory network (GRN) describing cell types and cell states became achievable. However, extracting key regulatory elements, including gene regulatory pathways (GRPs), transcription factors (TFs), and targetomes, that accurately and completely reflects functionality changes in biological phenomena remains challenging. Herein, we describe AGEAS, an semi-supervised automated machine learning (AutoML) based genetic regulatory element extraction system that assesses importances of GRPs in resulting biological phenomena, such as cell type differentiation, physiological and pathological development, and reconstructs GRNs with extracted important GRPs for comprehensive inference. With several case studies in divergent research areas, we show that AGEAS can indeed extract informative regulatory elements and reconstruct networks to indicate regulatory changes in biological phenomena of interest. Availability and implementationThe AGEAS code is available at https://github.com/JackSSK/Ageas.

bioinformatics↗

bioRxiv2022

HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used single particle cryo-electron microscopy with a retrovirus to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 [A] resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 [A] resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.

microbiology↗

bioRxiv2022

Hedgehogs are the major amplifying hosts of severe fever with thrombocytopenia syndrome virus

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne bandavirus mainly transmitted by Haemaphysalis longicornis in East Asia, mostly in rural areas. To date, the amplifying host involved in the natural transmission of SFTSV remains unidentified. Our epidemiological field survey conducted in endemic areas in China showed that hedgehogs were widely distributed, had heavy tick infestations, and had high SFTSV seroprevalence and RNA prevalence. After experimental infection of Erinaceus amurensis and Atelerix albiventris hedgehogs with SFTSV, robust but transitory viremias were detected, which lasted for around nine to eleven days. The infected hedgehogs experienced light weight loss and histopathology of the spleen showed hemorrhagic necrosis and lymphopenia, with infected hedgehogs recovering after viral clearance. Remarkably, SFTSV transmission cycle between hedgehogs and nymph/adult H. longicornis was easily accomplished under laboratory condition with 100% efficiency. Furthermore, naive H. longicornis ticks could be infected by SFTSV-positive ticks co-feeding on naive hedgehogs, with transstadial transmission of SFTSV also confirmed. We also found that SFTSV viremia remained high in hedgehogs during hibernation, suggesting that this mechanism might contribute to the persistence of SFTSV from one year to the next. Of concern, we recently found evidence of the natural circulation of SFTSV in the urban area of Beijing City in China involving H. longicornis ticks and E. amurensis hedgehogs. Our study suggests that the hedgehogs are the major wildlife amplifying hosts of SFTSV and that urban outbreaks of SFTSV might occur in the future.

microbiology↗

bioRxiv2022

A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus

Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. We show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes allowed us to develop assays that will ensure the inclusion of these two genes in the wheat cultivars to forestall the recurrence of blast host jumps.

plant biology↗

bioRxiv2022

Control of Leaf Width by the APC/CTAD1-WL1-NAL1 Pathway in Rice

Leaf morphology is one of the most important features of the ideal plant architecture. However, the genetic and molecular mechanisms controlling leaf morphology in crops remain largely unknown, despite their central importance. Here we demonstrate that the APC/CTAD1-WL1-NAL1 pathway regulates leaf width in rice, and mutation of WL1 leads to width leaf variation. WL1 interacts with TAD1 and is degraded by APC/CTAD1, with the loss of TAD1 function resulting in narrow leaves. The WL1 protein directly binds to the regulatory region of NAL1 and recruits the corepressor TOPLESS-RELATED PROTEIN to inhibit NAL1 expression by down-regulating the level of histone acetylation of chromatin. Furthermore, biochemical and genetic analyses revealed that TAD1, WL1, and NAL1 function in a common pathway to control leaf width. Our study establishes an important framework for the APC/CTAD1-WL1-NAL1 pathway-mediated control of leaf width in rice and introduces novel perspectives for using this regulatory pathway for improving crop plant architecture.

plant biology↗

bioRxiv2022

Stem embolism vulnerability curve depends on methods used: is there a fifth mechanism of cavitation?

A long-established ecological paradigm predicts a functional relationship determining vulnerability to cavitation: vulnerability increases with vessel hydraulic efficiency and vessel diameter. Even within a species, big vessels cavitate before small ones. Some centrifuge methods for measuring vulnerability are prone to artifacts due to nano-particles seeding early embolism, as the particles are drawn into vessels during measurements. Both the Sperry and Cochard rotors are prone to early cavitation due to nano-particles drawn into long and wide vessels in Robinia pseudoacacia and Quercus acutissima, whereas extraction centrifuge methods produce vulnerability curves more resistant to cavitation. Sufficient nano-particles pass through the stems to seed early embolism in all rotor designs. For several years, people have thought that early embolism is induced by nano-particles present in laboratory water. One new hypothesis is that the origin of nano-particles is from cut-open living cells but a much bigger study including many species is required to confirm this idea. This paper confirms the hypothesis in comparisons between short-vesselled Acer, and long-vesselled Robinia, and Quercus. Our new results and a review of old results justifies bigger study. Hypothetical nano-particles might explain why different methods for measuring vulnerability curves cause different T50 = tensions causing 50% loss of hydraulic conductivity. Hence the hypothesis for future research should be that the open-vessel artifact is consistent with long vessels surrounded by cut open living cells. One sentence SummaryNano-particles induced early cavitation in species with vessel lengths about [1/4] the stem length used in all centrifuge rotors, and the origin of nano-particles might be from living cells nearby vessels

physiology↗

bioRxiv2022

Robust expansion of phylogeny for fast-growing genome sequence data

Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm TIPars by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.

bioinformatics↗

bioRxiv2021

Activation of retinoic acid receptor reduces metastatic prostate cancer bone lesions through blocking endothelial-to-osteoblast transition

Metastatic prostate cancer (PCa) in bone induces bone-forming lesions that contribute to progression and therapy resistance. Currently strategies targeting PCa-induced bone formation are lacking. We previously showed that PCa-induced bone originates from endothelial cells (EC) that have undergone endothelial-to-osteoblast (EC-to-OSB) transition in response to tumor-secreted BMP4. Here, we show that activation of retinoic acid receptor (RAR) inhibits EC-to-OSB transition and reduces PCa-induced bone formation. We found that palovarotene, a RAR{gamma} agonist being tested for heterotopic ossification in fibrodysplasia ossificans progressiva, inhibited EC-to-OSB transition and osteoblast mineralization in vitro, and decreased tumor-induced bone formation and tumor growth in several osteogenic PCa models. RAR/{beta}/{gamma} isoform knockdown in 2H11 ECs blocked EC-to-OSB transition and osteoblast mineralization. Pan-RAR agonist ATRA inhibited MycCaP-BMP4-induced bone formation and tumor growth under castration. Furthermore, palovarotene or ATRA reduced plasma Tenascin C, a factor secreted by EC-OSB cells, which may be used to monitor treatment response. Mechanistically, BMP4-activated pSmad1 forms a complex with RAR in the nucleus of 2H11 cells. RAR activation by palovarotene or ATRA causes pSmad1 degradation by recruiting E3-ubiquitin ligase Smurf1 into the nuclear pSmad1/RAR{gamma} complex. Our findings suggest that palovarotene can be repurposed to target PCa-induced bone formation to improve clinical outcomes for bone metastasis.

cancer biology↗

bioRxiv2021

A lung targeted miR-29 Mimic as a Therapy for Pulmonary Fibrosis

microRNAs are non-coding RNAs that negatively regulate gene networks. Previously, we reported a systemically delivered miR-29 mimic MRG-201 that reduced fibrosis in animal models, but at doses prohibiting clinical translation. Here, we generated MRG-229, a next-gen miR-29 mimic with improved chemical stability, conjugated with the internalization moiety BiPPB (PDGFbetaR-specific bicyclic peptide). In TGF-b-treated human lung fibroblasts and precision cut lung slices, MRG-229 decreased COL1A1 and ACTA2 gene expression and reduced collagen production. In bleomycin-treated mice, intravenous or subcutaneous delivery of MRG-229 downregulated profibrotic gene programs at doses more than ten-fold lower than the original compound. In rats and non-human primates, and at clinically relevant doses, MRG-229 was well tolerated, with no adverse findings observed. In human peripheral blood decreased mir-29 concentrations were associated with increased mortality in two cohorts potentially identified as a target population for treatment. Collectively, our results provide support for the development of MRG-229 as a potential therapy in humans with IPF. One Sentence SummaryOne Sentence Summary: A stabilized, next-generation miR-29 mimic has been developed that demonstrates efficacy at commercially viable doses with a robust safety margin in non-human primates.

molecular biology↗