Biology subjects

Jiang, B.

Publications and source records attributed to Jiang, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Deciphering the molecular mechanisms of FET fusion oncoprotein-DNA hollow co-condensates

Biomolecules such as nucleic acids and proteins can undergo liquid-liquid phase separation to form biomolecular condensates with diverse architectures. However, fundamental questions surrounding the biophysical principles that govern condensate architecture and their potential biotechnological applications remain unresolved. Here, we report that the FUS/EWS/TAF15 family fusion oncoprotein FUS-ERG forms hollow co-condensates with double-stranded DNA containing GGAA microsatellites. Through a combination of biochemical assays, super-resolution imaging, and mathematical modeling, we reveal that the interior surface of hollow co-condensates exhibits properties distinct from those of the external surface, a phenomenon we term nested asymmetric phase separation. Furthermore, we demonstrate that the self-organization and morphology control of FUS-ERG hollow co-condensates can be harnessed for DNA-based information manipulation, enabling targeted DNA deletion within dsDNA libraries and facilitating dynamic, hierarchical data selection. These findings provide critical insights into the biophysical mechanisms underlying multicomponent phase-separated cellular bodies and establish a foundation for leveraging condensate morphology in biotechnology.

biophysics↗

bioRxiv2025

RFdiffusion Exhibits Low Success Rate in De Novo Design of Functional Protein Binders for Biochemical Detection

The design of high-affinity protein binders is critical for biochemical detection, yet traditional methods remain labor-intensive. AI-driven tools like RFdiffusion, a RoseTTAFold-based diffusion model, offer promising alternatives for generating protein structures with tailored binding interfaces. This study evaluates RFdiffusions efficacy in designing de novo binders for six targets: Strep-Tag II (a peptide tag) and five eukaryotic proteins (STAT3, FGF4, EGF, PDGF-BB, and CD4). Five binders were designed for each target and experimentally validated. While two Strep-Tag II binders outperformed streptavidin in Western blot assays, none matched the sensitivity of anti-Strep-Tag II antibodies. Binders for the other targets failed due to low expression, nonspecific binding, or undetectable affinity. Despite generating structurally diverse candidates, RFdiffusions success rate was limited by low-affinity designs and inconsistent recombinant expression. These results underscore the need for further optimization of AI-driven protein design tools for practical biochemical applications.

bioengineering↗

bioRxiv2024

GOBoost: Leveraging Long-Tail Gene Ontology Terms for Accurate Protein Function Prediction

MotivationWith the advancement of deep learning, researchers have increasingly proposed computational methods based on deep learning techniques to predict protein function. However, many of these methods treat protein function prediction as a multi-label classification problem, often overlooking the long-tail distribution of functional labels (i.e., Gene Ontology Terms) in datasets. To address this issue, we propose the GOBoost method, which incorporates the proposed long-tail optimization ensemble strategy. Besides, GOBoost introduces the proposed global-local label graph module and multi-granularity focal loss function to enhance long-tail functional information, mitigate the long-tail phenomenon, and improve overall prediction accuracy. ResultsWe evaluate GOBoost and other state-of-the-art (SOTA) protein function prediction methods on the PDB and AF2 datasets. The GOBoost outperformed SOTA methods across all evaluation metrics on both datasets. Notably, in the AUPR evaluation on the PDB test set, GOBoost improved by 10.71%, 35.91%, and 22.71% compared to the SOTA HEAL method in the MF, BP, and CC functions. The experimental results demonstrate the necessity and superiority of designing models from the label long-tail distribution perspective. Availabilityhttps://github.com/Cao-Labs/GOBoost Contactcaora@plu.edu

bioinformatics↗

bioRxiv2024

Understanding disease-associated metabolic changes in human colon epithelial cells using iColonEpithelium metabolic reconstruction

The colon epithelium plays a key role in the host-microbiome interactions, allowing uptake of various nutrients and driving important metabolic processes. To unravel detailed metabolic activities in the human colon epithelium, our present study focuses on the generation of the first cell-type specific genome-scale metabolic model (GEM) of human colonic epithelial cells, named iColonEpithelium. GEMs are powerful tools for exploring reactions and metabolites at systems level and predicting the flux distributions at steady state. Our cell-type-specific iColonEpithelium metabolic reconstruction captures genes specifically expressed in the human colonic epithelial cells. The iColonEpithelium is also capable of performing metabolic tasks specific to the cell type. A unique transport reaction compartment has been included to allow simulation of metabolic interactions with the gut microbiome. We used iColonEpithelium to identify metabolic signatures associated with inflammatory bowel disease. We integrated single-cell RNA sequencing data from Crohns Diseases (CD) and ulcerative colitis (UC) samples with the iColonEpithelium metabolic network to predict metabolic signatures of colonocytes between CD and UC compared to healthy samples. We identified reactions in nucleotide interconversion, fatty acid synthesis and tryptophan metabolism were differentially regulated in CD and UC conditions, which were in accordance with experimental results. The iColonEpithelium metabolic network can be used to identify mechanisms at the cellular level, and our network has the potential to be integrated with gut microbiome models to explore the metabolic interactions between host and gut microbiota under various conditions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/619644v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@77e2deorg.highwire.dtl.DTLVardef@cf7de2org.highwire.dtl.DTLVardef@51c178org.highwire.dtl.DTLVardef@174e2c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Intranasal Lithium Chloride Nanoparticles Inhibit Inflammatory Pyroptosis in Brains and Ameliorate Memory Loss and Depression Behavior in 5xFAD mice

BackgroundAlzheimers disease (AD) is a devastating neurodegenerative disease (AD) and has no treatment that can cure or halt the disease progression. This study explored the therapeutic potential of lithium salt dissolved in Ryanodex formulation vehicle (RFV) and delivered to the brain by intranasal application. We first compared lithium concentrations in the brain and blood of wild-type mice following intranasal or oral administration of lithium chloride (LiCl) dissolved in either RFV or water. The beneficial and side effects of intranasal versus oral LiCl in RFV in these mice were assessed and potential mechanisms underlying the efficacy of anti-inflammation and anti-pyroptosis in the brains were also investigated in both wild-type (WT) and 5XFAD Alzheimers Disease (AD) mice brains. MethodsFor the study of brain versus blood lithium concentrations, WT B6SJLF1/J mice at 2 months of age were treated with intranasal or oral LiCl (3 mmol/kg) dissolved in RFV or in water. Brain and blood lithium concentrations were measured at various times after drugs administration. Brain/blood lithium concentration ratios were then determined. For studying therapeutic efficacy versus side effects and their underlying mechanisms, 5XFAD and WT B6SJLF1/J mice were treated with intranasal LiCl (3 mmol/kg) daily, Monday to Friday each week, in RFV beginning at 2 or 9 months of age with a 12-week treatment duration. Animal behaviors were assessed for depression (tail suspension), cognition (fear conditioning and Y maze), olfaction (buried food test), and motor functions (rotarod) at the age of 5 and 12 months. Blood and brain tissue were harvested from these mice at 13 months. Blood biomarkers for the functions of thyroid (thyroid stimulating hormone, TSH) and kidney (creatinine) were measured using ELISA. Changes in protein expression levels of the endoplasmic reticulum Ca2+ release channels type 1 InsP3 receptors (InsP3R-1), malondialdehyde (MDA)-modified proteins and 4-hydroxy-2-nonenal (4-HNE), pyroptosis regulatory proteins (NLR family pyrin domain containing 3 (NLRP3), cleaved caspase-1, N-terminal of Gasdermin D (GSDMD)), cytotoxic (IL-1{beta}, IL-18, IL-6, TNF-) and cytoprotective (IL-10) cytokines and synapse proteins (PSD-95, synapsin-1) were determined using immunoblotting. Mouse body weights were monitored regularly. ResultsCompared to oral LiCl in RFV nanoparticles, intranasal treatment of WT mice with LiCl in RFV markedly decreased blood concentrations at the time frame of 30-120 minutes. The ratio of brain/blood lithium concentration after Intranasal lithium chloride in RFV significantly increased, in comparison to those after oral administration lithium chloride in RFV or intranasal administration of lithium chloride in water. Intranasal lithium chloride in RFV inhibited both memory loss and depressive behavior in adult and aged 5XFAD mice. Additionally intranasal treatment of aged 5XFAD mice with LiCl in RFV effectively suppressed the increases in InsP3R-1, intracellular oxidative stress markers (4-HNE-bound and MDA-modified proteins), pyroptosis activation proteins (NLRP3, cleaved caspase-1, N-terminal GSDMD) and cytotoxic cytokines (IL-1{beta}, IL-6, TNF-), but reversed the down-regulation of cytoprotective cytokine IL-10. Intranasal LiCl in RFV also alleviated the loss of the postsynaptic synapse protein PSD-95, but not synapsin-1, in aged 5XFAD mice. Blood level of the kidney function marker creatinine was significantly increased in 5XFAD than in WT mice in an age-dependent manner and this elevation was abolished by intranasal delivery of LiCl in RFV. Intranasal LiCl in RFV for 12 weeks in both WT or 5XFAD mice did not affect blood biomarkers for thyroid function, nor did it affect smell or muscle function or body weight. ConclusionIntranasal administration of LiCl in RFV significantly decreased lithium blood concentrations and increased brain/blood lithium concentration ratio, in comparison to its oral administration. Intranasal administration of LiCl in RFV robustly protected against both memory loss and depressive-like behavior, while had no side effects concerning thyroid and kidney toxicity in 5XFAD mice. These lithium-induced beneficial effects were strongly associated with lithiums suppression of InsP3R-1 Ca2+ channel receptor increase, pathological neuroinflammation and activation of the pyroptosis pathway, as well as the loss of some synaptic proteins. Intranasal delivery of lithium salt in RFV could become an effective and potent inhibitor of pathological inflammation/pyroptosis in the CNS and serve as a new treatment for both AD-associated dementia and depression with minimal unwanted side effects including peripheral organ toxicity.

neuroscience↗

bioRxiv2024

Survival of hepatocytes from executioner caspase activation promotes liver regeneration by enhancing JAK/STAT3 activity

Activation of executioner caspases, which is a key step in the apoptotic process, has been reported to promote tissue regeneration by sending pro-proliferation signals to the surrounding cells. However, whether executioner caspase activation (ECA) has cell-autonomous effect on tissue regeneration is not clear. Here, by generating transgenic mice carrying a lineage tracing system for cells that have experienced ECA, we demonstrate that transient ECA occurs in hepatocytes during liver regeneration after partial hepatectomy (PHx) or carbon tetrachloride (CCl4) treatment. Instead of committing apoptotic cell death, the majority of hepatocytes with ECA survive and proliferate to contribute to liver regeneration. Interestingly, inhibition of ECA in livers results in reduced hepatocyte proliferation and impaired regeneration, whereas increasing ECA to a level sufficient to kill hepatocytes also impedes regeneration, suggesting that ECA needs to be precisely controlled during liver regeneration. Mechanistic studies show that ECA promotes hepatocyte proliferation during regeneration through enhancing JAK/STAT3 activity. Our work reveals an essential role of survival of hepatocytes from ECA in liver regeneration.

developmental biology↗

bioRxiv2024

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of various external stimuli. One key cellular strategy that enables these functions is stochastic gene expression programs. However, understanding how transcriptional bursting, and consequently, cell fate, responds to DNA damage on a genome-wide scale poses a challenge. In this study, we propose an interpretable and scalable inference framework, DeepTX, that leverages deep learning methods to connect mechanistic models and scRNA-seq data, thereby revealing genome-wide transcriptional burst kinetics. This framework enables rapid and accurate solutions to transcription models and the inference of transcriptional burst kinetics from scRNA-seq data. Applying this framework to several scRNA-seq datasets of DNA-damaging drug treatments, we observed that fluctuations in transcriptional bursting induced by different drugs was associated with distinct fate decisions: IdU treatment was associated with differentiation in mouse embryonic stem cells by increasing the burst size of gene expression, while low- and high-dose 5FU treatments in human colon cancer cells were associated with changes in burst frequency that corresponded to apoptosis- and survival-related fate, respectively. Together, these results show that DeepTX enables genome-wide inference of transcriptional bursting from single-cell transcriptomics data and can generate hypotheses about how bursting dynamics relate to cell fate decisions.

systems biology↗

bioRxiv2024

Acute BRCAness Induction and AR Signaling Blockage through CDK12/7/9 Degradation Enhances PARP Inhibitor Sensitivity in Prostate Cancer

Current treatments for advanced prostate cancer (PCa) primarily target the androgen receptor (AR) pathway. However, the emergence of castration-resistant prostate cancer (CRPC) and resistance to AR pathway inhibitors (APSIs) remains ongoing challenges. Here, we present BSJ-5-63, a novel proteolysis-targeting chimera (PROTAC) targeting cyclin-dependent kinases (CDKs) CDK12, CDK7, and CDK9, offering a multi-pronged approach to CRPC therapy. BSJ-5-63 degrades CDK12, diminishing BRCA1 and BRCA2 expression and inducing a sustained "BRCAness" state. This sensitizes cancer cells to PARP inhibitors (PARPis) regardless of their homologous recombination repair (HRR) status. Furthermore, CDK7 and CDK9 degradation attenuates AR signaling, enhancing its therapeutic efficacy. Preclinical studies, including both in vitro and in vivo CRPC models, demonstrate that BSJ-5-63 exerts potent anti-tumor activity in both AR-positive and AR-negative setting. This study introduces BSJ-5-63 as a promising therapeutic agent that addresses both DNA repair and AR signaling mechanisms, with potential benefits for a board patient population.

cancer biology↗

bioRxiv2024

Gut-resident C. perfringens impedes rotavirus vaccine efficacy

Background & AimsThe extent to which live orally-administered rotavirus (RV) vaccines elicit protective immunity is highly heterogeneous. We hypothesized microbiota composition might influence vaccine efficacy. MethodsWe tested this concept by examining extent to which colonizing mice with segmented filamentous bacteria (SFB) influenced RV vaccine efficacy.Influence of human microbiomes on RV vaccination was studied via administering germ-free mice fecal microbial transplants (FMT) from children with robust or minimal RV vaccine responsiveness. Post-FMT, mice were subjected to vaccination and challenge doses of RV. ResultsSFB administration resulted in a phenotype reminiscent of RV vaccine failure, i.e. minimal generation of RV antigens and, consequently, lack of anti-RV antibodies resulting in proneness to RV challenge once SFB levels diminished. Transplant of microbiomes from children to mice recapitulated donor vaccination phenotype. Specifically, mice receiving FMT from high-responding children exhibited high levels of fecal RV antigen shedding and RV antibodies in response to RV vaccination and, concomitantly, were impervious to RV challenge. In contrast, mice receiving FMT from children who had not responded to RV vaccination exhibited only modest responses to RV challenge and, accordingly, remained prone to RV challenge. Microbiome analysis ruled out a role for SFB but suggested that RV vaccine failure might involve Clostridium perfringens. Oral administration of cultured C. perfringens to gnotobiotic mice partially recapitulated the RV vaccine non-responder phenotype. Analysis of previously-reported microbiome data found C. perfringens abundance in children associated with RV vaccine failure. ConclusionMicrobiota composition influences RV vaccine virus infection and, consequently, protective immunity. C. perfringens may be one, perhaps of many, bacterial species harbored in the intestine of RV-vaccine non-responders that influences RV vaccine outcomes.

immunology↗

bioRxiv2024

The novel role of Kallistatin in linking metabolic syndromes and cognitive memory deterioration by inducing amyloid-β plaques accumulation and tau protein hyperphosphorylation

Accumulation of amyloid {beta} (A{beta}) peptides and hyperphosphorylated tau proteins in the hippocampus triggers cognitive memory decline in Alzheimers disease (AD). The incidence and mortality of sporadic AD were tightly associated with diabetes and hyperlipidemia, while the exact linked molecular is uncertain. Here, we reported that serum Kallistatin concentrations were meaningfully higher in AD patients, with a higher concentration of fasting blood glucose and triglyceride. In addition, the constructed Kallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype and lower LTP in hippocampal CA1 neurons accompanied by increased A{beta} deposition and tau phosphorylation. Mechanistically, Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling, resulting in A{beta} cleavage and production. Besides, Kallistatin could promote the phosphorylation of tau by activating GSK-3{beta}. Fenofibrate, a hypolipidemic drug, could alleviate cognitive memory impairment by down-regulating A{beta} and tau phosphorylation of KAL-TG mice. Collectively, our data clarified a novel mechanism for A{beta} accumulation and tau protein hyperphosphorylation regulation by Kallistatin, which might play a crucial role in linking metabolic syndromes and cognitive memory deterioration, and suggested that fenofibrate might have the potential for treating metabolism-related AD. HighlightsO_LIKallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype accompanied by increased A{beta} deposition and tau phosphorylation. C_LIO_LIKallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling. C_LIO_LIFenofibrate could alleviate cognitive memory impairment and down-regulate the serum Kallistatin level. C_LI

neuroscience↗

bioRxiv2024

Heterogeneous Cardiac- and Neural Crest-Derived Aortic Smooth Muscle Cells have Similar Transcriptional Changes after TGFβ Signaling Disruption

Smooth muscle cells (SMCs) of cardiac and neural crest origin contribute to the developing proximal aorta and are linked to disease propensity in adults. We analyzed single-cell transcriptomes of SMCs from mature thoracic aortas in mice to determine basal states and changes after disrupting transforming growth factor-{beta} (TGF{beta}) signaling necessary for aortic homeostasis. A minority of Myh11 lineage-marked SMCs differentially expressed genes suggestive of embryological origin. Additional analyses in Nkx2-5 and Wnt1 lineage-marked SMCs derived from cardiac and neural crest progenitors, respectively, showed both lineages contributed to a major common cluster and each lineage to a minor distinct cluster. Common cluster SMCs extended from root to arch, cardiac subset cluster SMCs from root to mid-ascending, while neural crest subset cluster SMCs were restricted to the arch. The neural crest subset cluster had greater expression of a subgroup of TGF{beta}-dependent genes suggesting specific responsiveness or skewed extracellular matrix synthesis. Nonetheless, deletion of TGF{beta} receptors in SMCs resulted in similar transcriptional changes among all clusters, primarily decreased extracellular matrix molecules and modulators of TGF{beta} signaling. Many embryological markers of murine aortic SMCs were not confirmed in adult human aortas. We conclude: (i) there are multiple subtypes of cardiac- and neural crest-derived SMCs with shared or distinctive transcriptional profiles, (ii) neural crest subset SMCs with increased expression of certain TGF{beta}-inducible genes are not spatially linked to the aortic root predisposed to aneurysms from aberrant TGF{beta} signaling, and (iii) loss of TGF{beta} responses after receptor deletion is uniform among SMCs of different embryological origins.

pathology↗

bioRxiv2024

Short-Term Disruption of TGFβ Signaling in Adult Mice Renders the Aorta Vulnerable to Hypertension-Induced Dissection

Hypertension and transient increases in blood pressure from extreme exertion are risk factors for aortic dissection in patients with age-related vascular degeneration or inherited connective tissue disorders. Yet, the common experimental model of angiotensin II-induced aortopathy in mice appears independent of high blood pressure as lesions do not occur in response to an alternative vasoconstrictor, norepinephrine, and are not prevented by co-treatment with a vasodilator, hydralazine. We investigated vasoconstrictor administration to adult mice 1 week after disruption of TGF{beta} signaling in smooth muscle cells. Norepinephrine increased blood pressure and induced aortic dissection by 7 days and even within 30 minutes that was rescued by hydralazine; results were similar with angiotensin II. Changes in regulatory contractile molecule expression were not of pathological significance. Rather, reduced synthesis of extracellular matrix yielded a vulnerable aortic phenotype by decreasing medial collagen, most dynamically type XVIII, and impairing cell-matrix adhesion. We conclude that transient and sustained increases in blood pressure cause dissection in aortas rendered vulnerable by inhibition of TGF{beta}-driven extracellular matrix production by smooth muscle cells. A corollary is that medial fibrosis, a frequent feature of medial degeneration, may afford some protection against aortic dissection.

pathology↗

bioRxiv2024

Fast and accurate modeling and design of antibody-antigen complex using tFold

Accurate prediction of antibody-antigen complex structures holds significant potential for advancing biomedical research and the design of therapeutic antibodies. Currently, structure prediction for protein monomers has achieved considerable success, and promising progress has been made in extending this achievement to the prediction of protein complexes. However, despite these advancements, fast and accurate prediction of antibody-antigen complex structures remains a challenging and unresolved issue. Existing end-to-end prediction methods, which rely on homology and templates, exhibit sub-optimal accuracy due to the absence of co-evolutionary constraints. Meanwhile, conventional docking-based methods face difficulties in identifying the contact interface between the antigen and antibody and require known structures of individual components as inputs. In this study, we present a fully end-to-end approach for three-dimensional (3D) atomic-level structure predictions of antibodies and antibody-antigen complexes, referred to as tFold-Ab and tFold-Ag, respectively. tFold leverages a large protein language model to extract both intra-chain and inter-chain residue-residue contact information, as well as evolutionary relationships, avoiding the time-consuming multiple sequence alignment (MSA) search. Combined with specially designed modules such as the AI-driven flexible docking module, it achieves superior performance and significantly enhanced speed in predicting both antibody (1.6% RMSD reduction in the CDR-H3 region, thousand times faster) and antibody-antigen complex structures (37% increase in DockQ score, over 10 times faster), compared to AlphaFold-Multimer. Given the performance and speed advantages, we further extend the capability of tFold for structure-based virtual screening of binding antibodies, as well as de novo co-design of both structure and sequence for therapeutic antibodies. The experiment results demonstrate the potential of tFold as a high-throughput tool to enhance processes involved in these tasks. To facilitate public access, we release code and offer a web service for antibody and antigen-antibody complex structure prediction, which is available at https://drug.ai.tencent.com/en.

bioinformatics↗

bioRxiv2024

Shrimp Hemocyanin elicits a potent humoral response in mammals and is favorable to hapten conjugation

Conjugation to a carrier protein is essential to give rise to the antigenicity of hapten, which is a small molecule and cannot induce an immune response by itself alone. Three carrier proteins e.g. KLH (Keyhole Limpet Hemocyanin), BSA (Bovine Serum Albumin), and OVA (Ovalbumin) were used mostly. KLH is advantageous to the others, majorly owing to its strong immunogenicity and limited usage in other biological assays. However, the solubility of KLH is not as well as the others, especially after hapten conjugation. Besides, the high market price of KLH results in high costs in vaccine and antibody development. Here, we extracted the shrimp hemocyanin (SHC) from Penaeus vannamei (P. vannamei) with a production yield of > 1 g proteins (98 % pure) per 1 kg shrimp. Compared to KLH, the peptide-SHC conjugates exhibit higher solubility after hapten conjugation. Furthermore, compared with KLH, SHC induces comparable antibody production efficiency in mammals, with or without conjugation. Finally, rabbit polyclonal antibodies or mouse monoclonal antibodies were generated by immunizing SHC-peptide conjugates, and their applications in western blot, immunofluorescence and immunohistochemistry were confirmed. Therefore, we demonstrated that SHC may be used as a substitute for KLH in future antibody and vaccine development.

bioengineering↗

bioRxiv2023

Co-existence of blaKPC-2 and blaVIM-2 in highly carbapenem-resistant Pseudomonas aeruginosa isolated in the ICU of a public hospital

In this study, highly carbapenem-resistant Pseudomonas aeruginosa (h-CRPA) 18102011 [the minimum inhibitory concentration (MIC) value of carbapenem antimicrobial imipenem (IP) for h-CRPA is 4,096 g/mL] was isolated from the bile of an intensive care unit (ICU) burn patient in China, and genomic sequencing revealed a complete genome. The genomes molecular characteristics were analyzed to assess the genetic environment of blaKPC-2 and blaVIM-2. Average nucleotide identity (ANI) comparisons were used for precise species-level identification, while serotyping, multi-locus sequence typing, and the identification of acquired resistance genes, and virulence genes were also carried out. The h-CRPA 18102011 strain carrying blaKPC-2 and blaVIM-2 was identified as strain ST2374 and the O4 serotype. Virulence genes (plcH, exoST) and resistance genes (aph(3)-IIb, aac(6)-Ib-cr, ant(2)-Ia, blaOXA-396, blaPAO, blaKPC-2, blaVIM-2, blaPER-1, sul1, catB7, qnrVC6, fosA) were both identified in the genome. In addition, the IncpRBL16 type mega-plasmid pP2011-1 carrying blaVIM-2 and the IncP6 type plasmid pP2011-2 carrying blaKPC-2 were identified in the strain. The genetic environment of blaVIM-2 and blaKPC-2 was specifically evaluated to assess their origins. blaVIM-2 was located in the region of In2075 (a novel type 1 integron) that was inserted into plasmid pP2011-1, this plasmid contained 3 novel recombination sites, as well as the typical recombination site 2 (umuC) observed for IncpRBL16 type plasmids. However, the core module Tn3-ISKpn27-blaKPC-{Delta}ISKpn6 was identified as the blaKPC-2 platform in plasmid pP2011-2. Conjugation experiments revealed that the plasmids pP2011-1 and pP2011-2 of the h-CRPA 18102011 strain could be transferred into Escherichia coli with a conjugation transfer efficiency of 10-6. The E. coli transconjugant carried blaKPC-2 and blaVIM-2 from the donor and the MIC value of IP to the E. coli transconjugant was 4,096 g/mL, which was the same as observed for the donor. Overall, this study revealed the molecular characteristics of a VIM-2 and KPC-2-co-producing strain that was typed as O4 and ST2374. The continuous monitoring of bacteria, such as the strain investigated here, that co-harbor different types of carbapenemase genes is critical for preventing the spread of these genes.

genomics↗

bioRxiv2023

Potential intrahospital dissemination of Pseudomonas aeruginosa carrying the blaIMP-1 gene within a Tn7-like transposon

We aimed to determine the molecular characteristics of carbapenem-resistant Pseudomonas aeruginosa 18081308 and 18083286 isolated from the urine and sputum of two Chinese patients respectively, and analyzed the formation mechanism of the genetic environment in which it carries blaIMP-1. Bacterial genome sequencing was carried out on strains 18081308 and 18083286 to obtain their whole genome sequence. Average nucleotide identity (ANI) was used for their precise species identification. Serotyping and multilocus sequence typing were performed. Furthermore, the acquired resistance genes, and virulence factors of these strains were identified. The carbapenem-resistant P. aeruginosa strains isolated in the present study were of sequence type ST865 and serotype O6. They all carried the same virulence factors (PLC, ExoSTY) and resistance genes (aacC2, tmrB, and blaIMP-1). Tn6411, a Tn7-like transposon carrying blaIMP-1, was found in both strains. Detailed genetic dissection was applied to this transposon to display the genetic environment of blaIMP-1. The aacC2-tmrB region remnant-Tn6411 backbone was the original structure of this type of transposon. A Tn402-like type 1 integron (intl1-aac(6)-II-blaIMP-1) was inserted into it and formed a stable structure, which was localized in the chromosome by TnsD for transmission within P. aeruginosa; the original structure of Tn7-like transposon was localized on the plasmid by TnsE for horizontal transmission between bacterial species. The intrahospital dissemination of P. aeruginosa ST865 isolated in this study was episodic. The blaIMP-1-carrying Tn7-like transposon might enhance their ability to survive under drug selection pressure and aggravate the difficulty in treating infections.

genomics↗

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

AMPK targets PDZD8 to trigger carbon source shift to glutamine

The shift of carbon utilisation from glucose to other nutrients is a fundamental metabolic adaptation to cope with the decreased glucose oxidation during fasting or starvation1. AMP-activated protein kinase (AMPK) plays crucial roles in manifesting physiological benefits accompanying glucose starvation or calorie restriction2. However, the underlying mechanisms are unclear. Here, we show that low glucose-induced activation of AMPK plays a decisive role in the shift of carbon utilisation from glucose to glutamine. We demonstrate that endoplasmic reticulum (ER)-localised PDZD8, which we identify to be a new substrate of AMPK, is required for the glucose starvation-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527), and promotes it to interact with and activate the mitochondrial glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis3-5, and as a result the ER-mitochondria contact is strengthened. In vivo, PDZD8 enhances glutaminolysis, and triggers mitohormesis that is required for extension of lifespan and healthspan in Caenorhabditis elegans subjected to glucose starvation or caloric restriction. Muscle-specific re-introduction of wildtype PDZD8, but not the AMPK-unphosphorylable PDZD8-T527A mutant, to PDZD8-/- mice is able to rescue the increase of glutaminolysis, and the rejuvenating effects of caloric restriction in aged mice, including grip strength and running capacity. Together, these findings reveal an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis and executes the anti-ageing effects of calorie restriction by promoting inter-organelle crosstalk between ER and mitochondria.

cell biology↗