Biology subjects

Sun, B.

Publications and source records attributed to Sun, B..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Extracellular Matrix Protein 1 Attenuates Hepatic Fibrosis by Inhibiting TSP-, ADAMTS-, and MMP-Mediated Latent TGF-β1 Activation

ObjectiveExtracellular Matrix Protein 1 (ECM1) serves as a gatekeeper of hepatic fibrosis by maintaining transforming growth factor-{beta}1 (TGF-{beta}1) in its latent form. ECM1 knockout (KO) causes latent (L) TGF-{beta}1 activation, resulting in hepatic fibrosis with rapid mortality. In chronic liver disease (CLD), ECM1 decreases with increasing CLD severity. We investigate the regulatory role of ECM1 in TGF-{beta}1 bioavailability and its impact on CLD progression. DesignRNAseq was performed to analyze hepatic gene expression. Functional assays were performed using hepatic stellate cells (HSCs), Ecm1-KO and Fxr-KO mice, patient liver tissue, and computer simulations. ResultsExpression of LTGF-{beta}1 activators, including thrombospondins (TSPs), ADAMTS proteases, and matrix metalloproteinases (MMPs) increased along with pro-fibrotic gene expression in liver tissue of Ecm1-KO mice. In HSCs, overexpression of ECM1 prevented TSP-1-, ADAMTS1-, and MMP-2/9-mediated LTGF-{beta}1 activation. In vitro interaction assays demonstrated that ECM1 inhibited LTGF-{beta}1 activation by interacting with TSP-1 and ADAMTS1 via their respective, intrinsic KRFK or KTFR amino acid sequences, and by suppressing MMP-2/9 proteolytic activity. In mice, ECM1 overexpression attenuated KRFK-induced LTGF-{beta}1 activation, while KTFR treatment reversed Ecm1-KO- and Fxr-KO-mediated liver injury. In patients with CLD, ECM1 expression was inversely correlated with TSP-1, ADAMTS1, MMP-2/9 expression and LTGF-{beta}1 activation. And these results were complemented by a computational compartment model representing the key network of cellular phenotypes and predicted interactions in liver fibrogenesis. ConclusionOur findings underscore the hepatoprotective effect of ECM1, which interferes with mediators of LTGF-{beta}1 activation, suggesting ECM1 or its representative peptide as potential anti-fibrotic therapies in CLD. What is already known on this topic?[tpltrtarr] ECM1 expression is negatively correlated with CLD progression. [tpltrtarr]ECM1 maintains liver homeostasis by keeping TGF-{beta}1 latency. What this study adds?[tpltrtarr] ECM1 inhibits LTGF-{beta}1 activation through interfering with key activators, including TSP-1, ADAMTS1, MMP-2, and MMP-9. [tpltrtarr]ECM1 interacts with TSP-1 and ADAMTS1 via their respective, intrinsic KRFK or KTFR amino acid motifs, and suppresses MMP-2/9 proteolytic activity. [tpltrtarr]In vivo, ECM1 overexpression mitigates KRFK peptide-induced LTGF-{beta}1 activation, while KTFR peptide rescues Ecm1-KO- and Fxr-KO-induced liver injury. [tpltrtarr]ECM1 expression inversely correlates with TSP-1, ADAMTS1, MMP-2/9 expression and LTGF-{beta}1 activation in CLD patients. How might this study affect research, practice or policy?[tpltrtarr] Considering severe adverse effects associated with anti-fibrotic treatments utilizing TGF-{beta}1 receptor inhibitors, our findings indicate that restoration of ECM1 expression or phenocopying peptides might represent a novel and safe route to urgently needed anti-fibrotic therapies in CLD.

cell biology↗

bioRxiv2023

Lithocholic acid targets TULP3 to activate sirtuins and AMPK to retard ageing

Lithocholic acid (LCA), accumulated in the body during calorie restriction (CR), can confer administered metazoans with the ability to activate AMP-activated protein kinase (AMPK) and retard ageing. However, how LCA is signalled to activate AMPK and elicit the biological effects is unclear. Here, we show that LCA can enhance sirtuins (SIRTs) to deacetylate and subsequently inhibit vacuolar H+-ATPase (v-ATPase), thereby triggering AMPK activation via the lysosomal glucose-sensing pathway. Through proteomic analysis of SIRT1-coimmunoprecipitated proteins, we identify and validate that TUB like protein 3 (TULP3) is a constitutive component of SIRTs. Surprisingly, we found that TULP3 is an LCA receptor, and that the LCA-bound TULP3 activates SIRTs. The activated SIRTs in turn deacetylate the V1E1 subunit of v-ATPase on K52, K99 and K191 residues. Muscle-specific expression of the 3KR mutant of V1E1, mimicking the deacetylated state, dominantly activates AMPK and rejuvenates muscles in aged mice. Moreover, LCA once administered also activates AMPK and extends lifespan and healthspan in nematodes and flies, depending on the TULP3 homologues tub-1 and ktub, respectively. Our study thus elucidates that LCA triggers the TULP3-sirtuin-v-ATPase- AMPK route to manifest benefits of calorie restriction.

physiology↗

bioRxiv2023

Behavioral adaptation to changing energy constraints via altered frequency of movement selection

Animal behavior is strongly constrained by energy consumption. A natural manipulation which provides insight into this constraint is development, where an animal must adapt its movement to a changing energy landscape as its body grows. Unlike many other animals, for fish it is relatively easy to estimate the energy consumed by their movements via fluid mechanics. Here we simulated the fluid mechanics of >100,000 experimentally-recorded movement bouts from larval zebrafish across different ages and fluid conditions as they hunted Paramecia. We find that these fish adapt to their changing relationship with the fluid environment as they grow by adjusting the frequency with which they select different types of movements, so that more expensive movements are chosen less often. This strategy was preserved when fish were raised in an unnaturally viscous environment. This work suggests a general principle by which animals could minimize energy consumption in the face of changing energy costs over development.

animal behavior and cognition↗

bioRxiv2023

Specificity and promiscuity of JAK recruitment regulates pleiotropy of cytokine-receptor signaling

Promiscuous binding of different Janus kinases (JAKs) to class I/II cytokine receptors has been reported, yet its role in signaling is unclear. To systematically explore JAK pairing in type I interferon (IFN-I) signaling, we generated an artificial IFN-I receptor (AIR) by replacing the extracellular domains of IFNAR1 and IFNAR2 with anti mEGFP and mCherry nanobodies. The heterodimeric AIR restored near-native IFN-I activity, while the homomeric variant of IFNAR2 (AIR-dR2) initiated much weaker signaling despite harboring docking sites for signal transducer and activator of transcription (STAT) proteins. AIR-dR1 was signaling inactive, yet, pulldown uncovered its ICD to bind both TYK2 and JAK1. To further investigate the roles of JAKs on the receptors, knockout (KO) JAK1, JAK2, TYK2, and JAK2/TYK2 were generated. JAK1 KO led to complete loss of IFN-I signaling, which was partially restored by TYK2 overexpression. TYK2 KO cells retained partial activity, which was elevated by JAK1 overexpression, suggesting both JAKs to partially substitute each other. Conversely, JAK2 KO only moderately impacted the biological activity of IFN-Is, even in JAK2/TYK2 KO cells. Live cell micropatterning confirmed promiscuous binding of JAK1, JAK2 and TYK2 to IFNAR1 and IFNAR2, in line with an AlphaFold model that shows JAKs interchangeability on IFNAR ICDs. Similar promiscuity of JAK binding was observed for TPOR and GHR but not EPOR, accompanied by different downstream signaling activity. The competitive binding of JAKs to cytokine receptors together with the highly diverse absolute and relative JAK expression levels can account for cell type-dependent signaling pleiotropy observed for cytokine receptors. One Sentence SummaryPromiscuous and interchangeable binding of JAKs to cytokine receptors enables cell type-specific pleiotropic signaling.

biochemistry↗

bioRxiv2023

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present the first Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar "Zhonghuang 13" (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

plant biology↗

bioRxiv2023

Reconciling ASPP-p53 Binding Mode Discrepancies through an Ensemble Binding Framework that Bridges Crystallography and NMR Data

ASPP2 and iASPP bind to p53 through their conserved ANK-SH3 domains to respectively promote and inhibit p53-dependent cell apoptosis. While crystallography has indicated that these two proteins employ distinct surfaces of their ANK-SH3 domains to bind to p53, solution NMR data has suggested similar surfaces. In this study, we employed multi-scale molecular dynamics (MD) combined with free energy calculations to reconcile the discrepancy in the binding modes. We demonstrated that the binding mode based solely on a single crystal structure does not enable iASPPs RT loop to engage with p53s C-terminal linker--a verified interaction. Instead, an ensemble of simulated iASPP-p53 complexes facilitates this interaction. We showed that the ensemble-average inter-protein contacting residues and NMR-detected interfacial residues align well with ASPP proteins, and the ensemble-average binding free energies better match experimental Kd values compared to single crystallgarphy-determined binding mode. For iASPP, the sampled ensemble complexes can be grouped into two classes, resembling the binding modes determined by crystallography and solution NMR. We thus propose that crystal packing shifts the equilibrium of binding modes towards the crystallographydetermined one. Lastly, we show that the ensemble binding complexes are sensitive to p53s intrinsically disordered regions (IDRs), attesting to experimental observations that these IDRs contribute to biological functions. Our results provide a dynamic and ensemble perspective for scrutinizing these important cancer-related protein-protein interactions (PPIs).

biophysics↗

bioRxiv2023

Single-cell immune multi-omics and repertoire analyses in pancreatic ductal adenocarcinoma reveal differential immunosuppressive mechanisms within different tumour microenvironments

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. Understanding the multiple mechanisms by which the tumour evades immune control, and how these mechanisms may be disrupted is critical to developing targeted immunotherapies. Previous studies have shown that higher lymphocyte infiltration is associated with better survival, and here we investigated what mediates these differences. We performed a comprehensive analysis of PDAC-associated immune cells using single cell multi-omics coupled with re-analysis of public PDAC scRNA-seq datasets. We introduce novel single-cell and repertoire analyses that have uncoupled diverse roles and contributions of various immune cell populations within different tumour microenvironments (TMEs). They revealed clear distinctions in the clonal characteristics among different patient groups, provided valuable insights into the mechanisms of immune cell migration and tissue adaptation underlying these disparities. These results point to differential CD4 polarisation of intra-tumoural T cells, differential B cell differentiation, GC reactions, antigen presentation pathways, and distinct cell-cell communication between the myeloid-enriched and adaptive-enriched groups. Overall, we identified two major distinct themes for future immune intervention within PDAC patients between those with higher adaptive versus myeloid immune cell infiltration.

immunology↗

bioRxiv2023

isGWAS: ultra-high-throughput, scalable and equitable inference of genetic associations with disease

Genome-wide association studies (GWAS) have proven a powerful tool for human geneticists to generate biological insights or hypotheses for drug discovery. Nevertheless, a dependency on sensitive individual-level data together with ever-increasing cohort sample sizes, numbers of variants and phenotypes studied put a strain on existing algorithms, limiting the GWAS approach from maximising potential. Here we present in-silico GWAS (isGWAS), a uniquely scalable algorithm to infer regression parameters in case-control GWAS from cohort-level summary data. For any sample size, isGWAS computes a variant-disease association parameter in [~]1 millisecond, or [~]11m variants in UK-Biobank within [~]4 minutes ([~]1500-fold faster than state-of-the-art). Extensive simulations and empirical tests demonstrate that isGWAS results are highly comparable to traditional regression-based approaches. We further introduce a heuristic re-sampling algorithm, leapfrog re-sampler (LRS), to extrapolate association results to semi-virtually enlarged cohorts. Owing to significant computational gains we anticipate a broad use of isGWAS and LRS which are customizable on a web interface.

genetics↗

bioRxiv2023

Introducing PandaNovo for practical large-scale de novo peptide sequencing

De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing model{pi} -HelixNovo based on Transformer architecture.{pi} -HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.

bioinformatics↗

bioRxiv2023

Reprogramming method does not impact the neuronal differentiation potential of 16p11.2 deletion patient iPSCs

A major impediment to the actualization of the induced pluripotent stem cell (iPSC)-based personalized medicine revolution is the lack of widely accepted standard operating procedures (SOPs) across different groups and institutions. The various methods employed can include choice of starting materials, reprogramming agents, and culture conditions, with each of these factors hypothesized to influence the reprogramming efficiency and transcriptional identity of iPSCs. As such, we systematically compared iPSC reprogramming procedures using cells derived from the somatic cells of three patients with 16p11.2 deletion syndrome (16p11.2del) and found remarkable similarity among the different methods. FACS analysis revealed that regardless of somatic cell type (fibroblast, lymphocyte, erythroblast), route of reprogramming factor introduction (mRNA, Sendai virus, episome), donor sex, or facility (Rutgers, NYSCF), 16p11.2del patient iPSCs were viable as high purity cultures expressing pluripotency marker proteins. This observation was supported at the transcript level by qPCR analysis, which demonstrated the ability for the iPSCs to differentiate into all three embryonic germ cell lineages after 12 days in culture as embryoid bodies. NGN2-mediated differentiation of these iPSCs produced functional neurons that formed active synaptic networks as revealed by multi-electrode array (MEA) recordings. Importantly, no group-wise comparisons among the reprogramming methods yielded consistent statistically significant differences, indicating that these procedures are equally capable of producing pluripotent stem cells that can efficiently differentiate into mature, functional neurons. This work highlights the utility of these reprogramming methods and supports the use of differentially reprogrammed iPSCs for direct comparative studies of human neurodevelopment.

developmental biology↗

bioRxiv2023

Alternative splicing of a potato disease resistance gene maintains homeostasis between development and immunity, and functions as a novel process for pathogen surveillance

Plants possess a robust and sophisticated innate immune system against pathogens. The intracellular receptors with nucleotide-binding, leucine-rich repeat (NLR) motifs recognize pathogen-derived effector proteins to trigger the immune response. To balance plant growth and rapid pathogen detection, NLR expression is precisely controlled in multifaceted ways. The alternative splicing (AS) of introns in response to infection is recurrently observed but poorly understood. Here we report that the potato NLR gene RB undergoes AS of its intron, resulting in two transcriptional isoforms, which coordinately regulate plant immunity and growth homeostasis. During normal growth, RB predominantly exists as intron-retained isoform RB_IR, encoding a truncated protein containing only the N-terminus of the NLR. Upon late blight infection, the pathogen induces intron splicing of RB, increasing the abundance of RB_CDS, which encodes a full-length and active R protein. By deploying the RB splicing isoforms fused with a luciferase reporter system, we identified IPI-O1 (also known as Avrblb1), the RB cognate effector, as a facilitator of RB AS. IPI-O1 directly interacts with potato splicing factor StCWC15, resulting in altered localization of StCWC15 from the nucleoplasm to the nucleolus and nuclear speckles. Mutations in IPI-O1 that eliminate StCWC15 binding also disrupt StCWC15 re-localization and RB intron splicing. Thus, our study reveals that StCWC15 serves as a surveillance facilitator sensing the pathogen-secreted effector, and regulates the trade-off between RB-mediated plant immunity and growth, expanding our understanding of molecular plant-microbe interactions. One-sentence summaryPotato resistance gene RB balances plant growth and immunity through AS (alternative splicing), while pathogen-secreted effector IPI-O1 mediates AS of RB by targeting the conserved splicing factor StCWC15, further increasing the RB_CDS expression level to activate immunity.

plant biology↗

bioRxiv2023

Deep sequencing of the T cell Receptor reveals common and reproducible CD8+ signatures of response to checkpoint immunotherapy

Immune checkpoint blockade (ICB) has markedly improved outcomes across a range of tumours, including metastatic melanoma (MM). However, peripheral biomarkers of response remain lacking and underlying mechanisms of action incompletely described. A number of studies have demonstrated the value of T cell receptor (TCR) repertoire analysis in determining associations with response, however identifying key groups of T cells based on their TCR usage has remained elusive. Here we performed deep sequencing of the TCR of CD8+ T cells isolated from peripheral blood of patients receiving ICB for MM (n=91) at multiple time points, along with healthy control samples (n=42) and resected tumour specimens (from n=7 patients). Using the GLIPH2 algorithm to cluster TCR based on putative shared antigen specificity, we describe groups of TCR which expand post-ICB in responding patients which we term Emergent Responder (ER) clones. We find that these ER clones are typically large and of a memory phenotype, with increased expression of genes encoding cytotoxic proteins. Analysis of tumours resected in advance of ICB demonstrates ER clones are enriched and expanded within the tumour compared to the periphery at pre-treatment. Significantly, we note the proportion of the peripheral repertoire occupied by ER clones strongly correlates with long-term clinical response. Clinical outcome further associated with HLA type and, crucially, can be validated across replication and independent datasets. This work provides the first-in-kind description of TCR-defined CD8+ T cells that mediate the response to ICB in MM, demonstrating the prognostic utility of the peripheral immune repertoire with potential widespread therapeutic and prognostic applications.

immunology↗

bioRxiv2023

Comprehensive Allergen Profile of Blomia tropicalis Provides Insights into the Component-Resolved Diagnosis of Mite Allergy

BackgroundBlomia (B.) tropicalis, as an important species of house dust mites (HDMs), plays a critical role in allergic diseases in tropical populations, but its allergen components are less investigated than those of other HDMs. Multiple omics methods have largely improved the identification of mite allergens. Here, we sought to identify a comprehensive allergen profile of B. tropicalis and advance the allergen component-resolved diagnosis (CRD) of mite allergy. MethodsReference mite allergen sequences were searched in a high-quality genome of B. tropicalis. Comparative analysis was performed for important allergen groups. ELISA was used to assess the allergenicities of recombinant proteins of specific allergens. ResultsA complete allergen profile of B. tropicalis was revealed, including thirty-seven allergen groups (up to Blo t 42). In-depth comparative analysis not only determined the homology of major allergen groups 5 and 21 but also shed light on the emergence and divergence of chitin-binding allergens. The specific Blo t 12 was identified to be a chitin-binding protein originating from the chitinase of allergen group 15. Immunoassays of recombinant proteins verified three novel allergens and the ELISA results suggested geographical differences in the B. tropicalis sensitization rate. ConclusionsThe comprehensive allergen profile revealed in B. tropicalis, the comparative analysis of allergen groups and the immunoassay assessment of recombinant proteins largely expanded our knowledge to B. tropicalis allergens and could ultimately benefit the CRD of HDM allergy.

immunology↗

bioRxiv2023

3D co-culture of macrophages and fibroblasts in a sessile drop chip for unveiling the role of macrophages in skin wound-healing

Three-dimension (3D) cell co-cultural spheroids exhibit enhanced cellular functions and they can mirror in-vivo microenvironments. Herein, a sessile drop chip was developed to construct 3D spheroids for mirroring the wound healing microenvironment. The sessile drop chip holds the superhydrophobic surface of each microwell which can facilitate cell suspensions transfer to spheroids through the offset of surface tension and gravity, and each microwell has a cylinder hole that offers adequate oxygen to spheroids. It was demonstrated that the 3T3 fibroblast spheroid and the 3T3 fibroblast/M2-type macrophage co-culture spheroid can be formed and remained the physiological activity within nine days. 3D morphology of spheroids was reconstructed using the transparent processing technology and Z-stack function of confocal microscopy. Characteristics of proliferation and differentiation were analyzed by using nano antibody-based 3D immunostaining assay. Results revealed that M2-type macrophages can promote the proliferation and differentiation of the 3T3 fibroblast spheroid. This study presented a novel affordable platform for developing 3D spheroids and provides a 3D model for investigating the macrophages-associated wound healing microenvironment.

bioengineering↗

bioRxiv2022

Ibex: Variational autoencoder for single-cell BCR sequencing.

SummaryB cells are critical for adaptive immunity and are governed by the recognition of an antigen by the B cell receptor (BCR), a process that drives a coordinated series of signaling events and modulation of various transcriptional programs. Single-cell RNA sequencing with paired BCR profiling could offer insights into numerous physiological and pathological processes. However, unlike the plethora of single-cell RNA analysis pipelines, computational tools that utilize single-cell BCR sequences for further analyses are not yet well developed. Here we report Ibex, which vectorizes the amino acid sequence of the complementarity-determining region 3 (cdr3) of the immunoglobulin heavy and light chains, allowing for unbiased dimensional reduction of B cells using their BCR repertoire. Ibex is implemented as an R package with integration into both the Seurat and Single-Cell Experiment framework, enabling the incorporation of this new analytic tool into many single-cell sequencing analytic workflows and multimodal experiments. Availability and ImplementationIbex is available as an R package at https://github.com/ncborcherding/Ibex. Reproducible code and data for the figure appearing in the manuscript are available at https://github.com/ncborcherding/Ibex.manuscript. A companion TCR-based approach is available at https://github.com/ncborcherding/Trex.

bioinformatics↗

bioRxiv2022

Multi-Omic Analysis of Tyrophagus putrescentiae Reveals Insights into the Allergen Complexity of Storage Mites

BackgroundThe storage mite Tyrophagus putrescentiae is one of the major mites causing allergies in Chinese and Korean populations, but its allergen profile in incomplete when compared with that of house dust mites. Multiple genome-based methods have been introduced into the allergen study of mites and have enabled a better understanding of these medically important organisms. ObjectiveWe sought to reveal a comprehensive allergen profile of Tyrophagus putrescentiae and advance the allergen study of storage mites. MethodsBased on a high-quality assembled and annotated genome, an in silico analysis was performed by searching reference sequences to identify allergens. Immunoassay ELISA assessed the allergenicities of recombinant proteins. MALDI-TOF mass spectrometry identified the IgE-binding proteins. Comparative genomics analysis was employed for the important allergen gene families. ResultsA complete allergen profile of Tyrophagus putrescentiae was revealed, including thirty-seven allergen groups (up to Tyr p 42). Among them, five novel allergens were verified using the sera of allergy patients. Massive allergen homologs were identified as the result of gene duplications in genome evolution. Proteomic identification again revealed a wide range of allergen homologs. In the NPC2 family and GSTs, comparative analysis shed light on the expansion and diversification of the allergen groups. ConclusionUsing multi-omic approaches, the comprehensive allergen profile including massive homologs was disclosed in Tyrophagus putrescentiae, which revealed the allergen complexity of the storage mite and could ultimately facilitate the component-resolved diagnosis.

immunology↗

bioRxiv2022

An R-R-type MYB transcription factor promotes nonclimacteric pepper fruit ripening pigmentation

Carotenoids act as phytohormones and volatile compound precursors that influence plant development and confer characteristic colours, affecting both the aesthetic and nutritional value of fruits. Carotenoid pigmentation in ripening fruits is highly dependent on developmental trajectories. Transcription factors incorporate developmental and phytohormone signalling to regulate the biosynthesis process. In contrast to the well-established pathways regulating ripening-related carotenoid biosynthesis in climacteric fruit, carotenoid regulation in nonclimacteric fruit is poorly understood. Capsanthin is the primary carotenoid of nonclimacteric pepper (Capsicum) fruit; its biosynthesis is tightly associated with fruit ripening, and it confers red pigment to the ripening fruit. In this study, using a weighted gene coexpression network and expression analysis, we identified an R-R-type MYB transcription factor, DIVARICATA1, and demonstrated that it is tightly associated with the levels of carotenoid biosynthetic genes (CBGs) and capsanthin accumulation. DIVARICATA1 encodes a nucleus-localized protein that functions primarily as a transcriptional activator. Functional analyses demonstrated that DIVARICATA1 positively regulates CBG transcript levels and capsanthin contents by directly binding to and activating the CBG promoter transcription. Furthermore, the association analysis revealed a significant positive association between DIVARICATA1 transcription level and capsanthin content. Abscisic acid (ABA) promotes capsanthin biosynthesis in a DIVARICATA1-dependent manner. Comparative transcriptomic analysis of DIVARICATA1 in pepper and its orthologue in a climacteric fruit, tomato, suggests that its function might be subject to divergent evolution among the two species. This study illustrates the transcriptional regulation of capsanthin biosynthesis and offers a novel target for breeding peppers with high red colour intensity.

plant biology↗

bioRxiv2022

TLR4/NF-κB Signaling Contributes to the Inflammation in Ovary and Inguinal Fats of Polycystic Ovary Syndrome

BackgroundPolycystic ovary syndrome (PCOS) is a complex reproductive endocrine disorder. It has highly heterogeneous clinical manifestations which are characterized by biochemical hyperandrogenemia, obesity, insulin resistance, dyslipidemia, anovulation, and polycystic ovaries. However, the etiologies of PCOS are still unclear. Recently, studies have found that the low-grade inflammation contributed to the occurrence of PCOS, and as a critical biomarker indicated the endocrine disruptions in PCOS. ObjectiveThis study is aimed to investigate the processes and mediators of inflammation in contributing to the development of PCOS. MethodsLetrozole (LET) induced PCOS rat model was used in this study. Body weight, body temperature, inguinal fats weight, fasting glucose level, ovarian morphology, NF-{kappa}B signaling target genes in ovary, and protein expression levels of TLR4 and NF-{kappa}B in ovarian and inguinal fats were measured in rats with placebo and LET administrations for 6 and 12 weeks. ResultsPCOS rats, especially with LET intervention for 12 weeks, had higher body weight, inguinal fats weight and fasting glucose level compared to control group. The protein expression levels of TLR4 and NF-{kappa}B in cytoplasm of ovarian and inguinal fats were increased in LET-induced PCOS rats compared to control groups, while NF-{kappa}B in nucleus were reduced in PCOS rats. The expressions of ACTB, C3, CXCL3, NQO1 and SELP in ovarian were statistically different in PCOS rats induced by LET compared to control groups. ConclusionThese findings indicated that stimulating TLR4/NF-{kappa}B pathway in inguinal fats and ovary tissues contributed to the increased inflammation in LET-induced PCOS rats, which, in turn, exacerbated the phenotype of PCOS including weight gain, adipose tissue accumulation, hyperglycemia and follicular dysplasia.

pathology↗