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Zhao, D.

Publications and source records attributed to Zhao, D..

At least 73 records · Page 4Linked to original sources

BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health

The liver is the largest solid organ in the body and is primarily composed of HCs, ECs, KCs, and HSCs, which spatially interact and cooperate with each other to maintain liver homeostasis. However, the complexity and molecular mechanisms underlying the crosstalk between these different cell types remain to be revealed. Here, we generated mice with conditional deletion of Bmp9/10 in different liver cell types and demonstrated that HSCs were the major source of BMP9 and BMP10 in the liver. Using transgenic ALK1 (receptor for BMP9/10) reporter mice, we found that ALK1 is expressed on KCs and ECs other than HCs and HSCs, and BMP9/10 secreted by HSCs promotes the differentiation of KCs and ECs and maintain their identity. Pdgfb expression was significantly upregulated in KCs and ECs after BMP9 and BMP10 deletion, ultimately leading to HSCs activation and liver fibrosis. ECs express several angiocrine factors, such as BMP2, BMP6, Wnt2 and Rspo3, to regulate hepatocyte iron metabolism and metabolic zonation. We found that these angiocrine factors were significantly decreased in ECs from Bmp9/10HSC-KO mice, which further resulted in liver iron overload and disruption of HC zonation. In summary, we demonstrated that HSCs play a central role in mediating liver cell-cell crosstalk via the production of BMP9/10, highlighting the important role of intercellular interaction in organ development and homeostasis.

cell biology↗

A systematic evaluation of computation methods for cell segmentation

Cell segmentation is a fundamental task in analyzing biomedical images. Many computational methods have been developed for cell segmentation and instance segmentation, but their performances are not well understood in various scenarios. We systematically evaluated the performance of 18 segmentation methods to perform cell nuclei and whole cell segmentation using light microscopy and fluorescence staining images. We found that general-purpose methods incorporating the attention mechanism exhibit the best overall performance. We identified various factors influencing segmentation performances, including image channels, choice of training data, and cell morphology, and evaluated the generalizability of methods across image modalities. We also provide guidelines for choosing the optimal segmentation methods in various real application scenarios. We developed Seggal, an online resource for downloading segmentation models already pre-trained with various tissue and cell types, substantially reducing the time and effort for training cell segmentation models.

bioinformatics↗

Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells

Type I CRISPR-Cas systems are widespread and have exhibited remarkable versatility and efficiency in genome editing and gene regulation in prokaryotes. However, due to the multi-subunit composition and large size, their application in eukaryotes has not been thoroughly investigated. Here, we demonstrate that the type I-F2 Cascade, the most compact among type I systems and significantly smaller than SpCas9, can be developed into programmable tools for use in human cells. For transcriptional activation, the efficiency of the tool based on the engineered I-F2 system can match or surpass that of dCas9. Besides, narrow editing windows limit the application of base editors. Although the R-loop formed by Cascade is much wider than that by Cas9 or Cas12, the potential of base editing with Cascade has not yet been explored. We successfully created a base editor with the I-F2 Cascade, which induces a considerably wide editing window ([~]30 nt) with a bimodal distribution. The wide editing window can expand the range of targetable sites and can be useful for disrupting functional sequences and genetic screening. The editing efficiency can achieve 50% in human cells. This research underscores the application potential of compact type I systems in eukaryotes and developed a new base editor with an extraordinary wide editing window.

molecular biology↗

Transcriptome Dynamics in Mouse Amygdala under Acute and Chronic Stress Revealed by Thio-labeled RNA Sequencing

Both acute and chronic stress have significant impact on brain functions. The amygdala is essential in mediating stress responses, but how its transcriptomic dynamics change under stress remains elusive. To overcome the difficulties in detecting subtle stress-induced changes by evaluating total RNA using classic RNA sequencing, we conducted thiol-labeled RNA sequencing (SLAM-seq). We injected 4-thiouridine (4sU) into mouse amygdala followed by SLAM-seq to detect nascent mRNA induced by acute and chronic restraint stress, and found that SLAM-seq could label actively transcribed genes in the major neuronal and glial subtypes. We also found that acute stress induced active transcription of 6 gamma-aminobutyric acid (GABA) receptors and only 1 glutamate receptor, indicating an imminent increase of inhibitory control in the stressed amygdala. Conversely, chronic stress led to active transcription of 3 glutamate receptors and 4 GABA receptors, suggesting a release of inhibitory control and hyperactivity of the amygdala. SLAM-seq also identified genes associated with myelination under chronic stress, and this finding is confirmed by immunostaining showing increased myelination in chronically stressed amygdala. Additionally, genes detected by SLAM-seq and RNA-seq only partially overlapped, with SLAM-seq particularly sensitive to transcriptional changes in genes with high basal transcription levels. Thus, by applying SLAM-seq in vivo, we obtained a rich dataset of nascently transcribed genes in the amygdala under stress, and revealed distinct transcriptional dynamics associated with acute and chronic stress.

neuroscience↗

A precision medicine approach for HCN1 Developmental and Epileptic Encephalopathy

Pathogenic variants in HCN1 causing cation leak result in a severe developmental and epileptic encephalopathy (DEE). Current treatment options for patients with HCN1-DEE are limited and are insufficient to fully address both the seizures and clinical comorbidities of this disorder. Org 34167 is a brain penetrant broad-spectrum HCN channel inhibitor that has completed phase I clinical trials. We used a range of assays at molecular, cellular, network and behavioural levels to explore the potential of Org 34167 as a precision medicine for HCN1-DEE. Org 34167 restored the voltage sensitivity of the DEE HCN1M305L mutated channel, significantly reducing cation leak. It also restored Ih-mediated sag, hyperpolarised the resting membrane potential and reduced firing of layer V neurons from the Hcn1M294L mouse model of HCN1-DEE, which was engineered based on the HCN1M305L pathogenic variant. Additionally, Org 34167 reduced neuronal epileptiform activity and restored retinal light sensitivity in these mice, suggesting it may improve both seizures and other clinical comorbidities. However, Org 34167-mediated tremors were noted at therapeutic doses. Org 34167 was also effective at reducing cation leak caused by five additional HCN1 pathogenic variants, suggesting broader utility. Overall, these data demonstrate that a small molecule HCN inhibitor can restore channel and consequent physiological functions, positioning it as a promising precision therapeutic approach for HCN1-DEE.

neuroscience↗

Eukfinder: a pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data.

Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities allows us to discover the functions, physiologies, and evolutionary histories of microbial prokaryote and eukaryote members of diverse ecosystems. Despite their importance, metagenomic studies of microbial eukaryotes lag behind those of prokaryotes, due to the difficulty in identifying and assembling high-quality eukaryotic genomes from WGS data. To address this problem, we have developed Eukfinder, a bioinformatics pipeline that recovers and assembles nuclear and mitochondrial genomes of eukaryotic microbes from WGS metagenomics data. As part of its workflow, it utilizes two specialized databases to classify reads based on taxonomy which can be customized to the dataset or environment of interest. We applied Eukfinder to human gut microbiome WGS metagenomic sequencing data to recover genomes from the protistan parasite Blastocystis sp., a highly prevalent colonizer of the gastrointestinal tract of humans and animals. We tested Eukfinder using both a series of simulated gut microbiome datasets, which included varying numbers of Blastocystis reads combined with bacterial reads and by using real metagenomic gut samples containing Blastocystis. We compared the results of Eukfinder with other published workflows. With sufficient reads, Eukfinder efficiently assembles high-quality near-complete nuclear and mitochondrial genomes from diverse Blastocystis subtypes from metagenomic data without the aid of a reference genome. Furthermore, with sufficient depth of sequence sampling, Eukfinder outperforms similar tools used to recover eukaryotic genomes from metagenomic data. Eukfinder will be a useful tool for reference-independent and cultivation-free study of eukaryotic microbial genomes from environmental metagenomic sequencing samples. IMPORTANCERapid advancements in next-generation sequencing technologies have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from samples taken from different environments. So far, thousands of new prokaryotic genomes have been characterized from strains or species that were unknown to science. However, the relatively large size and complexity of protistan genomes has, until recently, precluded the use of the WGS metagenomic approach to sample microbial eukaryotic diversity. The bioinformatics pipeline we developed, Eukfinder, can recover eukaryotic microbial genomes from environmental WGS metagenomic samples. By retrieving high-quality protistan genomes from diverse metagenomic samples, we can increase numbers of reference genomes available to aid future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and a variety of other ecosystems.

bioinformatics↗

State-transition Modeling of Blood Transcriptome Predicts Disease Evolution and Treatment Response in Chronic Myeloid Leukemia (CML)

Chronic myeloid leukemia (CML) is initiated and maintained by BCR::ABL which is clinically targeted using tyrosine kinase inhibitors (TKIs). TKIs can induce long-term remission but are also not curative. Thus, CML is an ideal system to test our hypothesis that transcriptome-based state-transition models accurately predict cancer evolution and treatment response. We collected time-sequential blood samples from tetracycline-off (Tet-Off) BCR::ABL-inducible transgenic mice and wild-type controls. From the transcriptome, we constructed a CML statespace and a three-well leukemogenic potential landscape. The potentials stable critical points defined observable disease states. Early states were characterized by anti-CML genes opposing leukemia; late states were characterized by pro-CML genes. Genes with expression patterns shaped similarly to the potential landscape were identified as drivers of disease transition. Re-introduction of tetracycline to silence the BCR::ABL gene returned diseased mice transcriptomes to a near healthy state, without reaching it, suggesting parts of the transition are irreversible. TKI only reverted the transcriptome to an intermediate disease state, without approaching a state of health; disease relapse occurred soon after treatment. Using only the earliest time-point as initial conditions, our state-transition models accurately predicted both disease progression and treatment response, supporting this as a potentially valuable approach to time clinical intervention even before phenotypic changes become detectable.

cancer biology↗

KRAS inhibition activates an actionable CD24 do-not-eat-me signal in pancreas cancer

KRASG12C inhibitors (G12Ci) have produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the function of KRASG12C and possible G12Ci bypass mechanisms, we developed an autochthonous KRASG12C- driven PDAC model. Compared to the classical KRASG12D PDAC model, the G12C model exhibits slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12C tumors produced modest impact despite stimulating a hot tumor immune microenvironment. Immunoprofiling revealed that CD24, a dont eat me signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Together, this study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC. SignificanceGeneration of an autochthonous KRASG12C-driven pancreatic cancer model enabled elucidation of specific effects of KRASG12C during tumor development, revealing CD24 as an actionable adaptive mechanism in cancer cells induced upon KRASG12C inhibition.

cancer biology↗

OBIA: An Open Biomedical Imaging Archive

With the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interface for data submission, browsing and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at https://ngdc.cncb.ac.cn/obia.

bioinformatics↗

Adapting to heat stress by sowing summer grain crops early in late winter: Sorghum root growth, water use, and yield

CONTEXTDrought and extreme heat at flowering are common stresses limiting the yield of summer crops, which are likely to intensify and become more frequent as projected under climate change. OBJECTIVEThis study explores the idea that adaptation to these stresses could be increased by sowing summer crops early in late winter or spring, to avoid the overlap with critical crop stages around flowering. Here we report on the impacts of early sowing i.e., in late winter and spring on sorghum crop and root growth and function (i.e., water use), and final grain yield. METHODSTwo seasons of on-farm genotype (G) by environment (E) by management (M) sorghum experimentation were conducted in the Darling Downs region of Queensland, Australia. Each trial consisted of a factorial combination of three times of sowing (TOS, referred to as late winter, spring, and summer), two levels of irrigation, four plant populations, and six commercial genotypes. Treatments were replicated three times. Crop roots and shoot were sampled at the flag leaf stage for each TOS. Crop water use across the growing season was monitored using time-lapse electromagnetic induction (EMI) surveys. EMI was also used to calculate a root activity factor. Final grain yield and yield components were determined at maturity. RESULTSResults showed that TOS, irrigation levels, and their interactions significantly influenced crop root and shoot traits, water use, and yield, though results were not always consistent across seasons. In the first season which was dry and had large temperature contrasts between TOS, crop growth in the early sown crops was primarily limited by temperature. In contrast, the second season was much warmer and crop growth was instead primarily limited by water availability. Cold air and soil temperatures in the early sowing dates i.e., late winter and spring during the first season, lead to smaller crops with smaller rooting systems and root-to-shoot ratios, and roots having a larger average root diameter. In general terms, root length and root length density responded positively to increasing pre-flowering mean air temperatures ranging between 16 and 20{degrees}C, while root average diameters were larger below 19 {degrees}C or above 21{degrees}C. Early sowing advanced flowering and therefore decreased the risk of extreme heat during the critical stages around flowering and affected water use before and after flowering. The root activity factor was directly related to the crop root length density. The early sown crops increased yield by transferring water use from vegetative to reproductive stages. The larger yield of the early sown crop was associated with larger grain numbers, particularly for the tillers, and a larger water use efficiency. As expected, irrigated and summer-sown crops exhibited lowest water use efficiency. The early-sown crops left more water in the soil profile at maturity, particularly under irrigated conditions and with small plant populations. CONCLUSIONSWe conclude that early sown sorghum is a potential option to increase crop adaptation to hotter and drier environments. Here we propose that in the race to increase crop adaptation to heat stresses, plant breeding efforts should consider cold tolerance traits during crop germination, emergence, and early vegetative stages so that sorghum sowing windows could be significantly advanced.

plant biology↗

Oxytocin alleviated colitis and colitis-associated colorectal tumorigenesis by targeting fucosylated MUC2

Colon cancer is commonly regarded as hormone-independent. However, there have been reports suggesting the involvement of sex hormones in colon cancer development. Nevertheless, the role of hormones from the hypothalamus-hypophysis axis in colitis-associated colorectal cancer (CAC) remains uncertain. In this study, we observed a significant reduction in the expression of the oxytocin receptor (OXTR) in colon samples from both colitis and CAC patients. To investigate further, we generated mice with an intestinal epithelium cell (IEC)-specific knockout of OXTR. These mice exhibited markedly increased susceptibility to dextran sulfate sodium (DSS)-induced colitis and DSS/Azoxymethane (AOM)-induced CAC compared to wild-type mice. Our findings indicate that OXTR depletion impaired the inner mucus of the colon epithelium. Mechanistically, oxytocin was found to regulate MUC2 maturation through B3GNT7-mediated fucosylation. Interestingly, we observed a positive correlation between B3GNT7 expression and OXTR expression in human colitis and CAC colon samples. Moreover, the administration of oxytocin significantly alleviated tumor burden. Hence, our study unveils oxytocins promising potential as an affordable and effective therapeutic intervention for individuals affected by colitis and CAC.

physiology↗

Anti-CD47 immunotherapy as a therapeutic strategy for the treatment of breast cancer brain metastasis

The presence of cell surface protein CD47 allows cancer cells to evade innate and adaptive immune surveillance resulting in metastatic spread. CD47 binds to and activates SIRP on the surface of myeloid cells, inhibiting their phagocytic activity. On the other hand, CD47 binds the matricellular protein Thrombospondin-1, limiting T-cell activation. Thus, blocking CD47 is a potential therapeutic strategy for preventing brain metastasis. To test this hypothesis, breast cancer patient biopsies were stained with antibodies against CD47 to determine differences in protein expression. An anti-CD47 antibody was used in a syngeneic orthotopic triple-negative breast cancer model, and CD47 null mice were used in a breast cancer brain metastasis model by intracardiac injection of the E0771-Br-Luc cell line. Immunohistochemical staining of patient biopsies revealed an 89% increase in CD47 expression in metastatic brain tumors compared to normal adjacent tissue (p [≤] 0.05). Anti-CD47 treatment in mice bearing brain metastatic 4T1br3 orthotopic tumors reduced tumor volume and tumor weight by over 50% compared to control mice (p [≤] 0.05) and increased IBA1 macrophage/microglia marker 5-fold in tumors compared to control (p [≤] 0.05). Additionally, CD47 blockade increased the M1/M2 macrophage ratio in tumors 2.5-fold (p [≤] 0.05). CD47 null mice had an 89% decrease in metastatic brain burden (p [≤] 0.05) compared to control mice in a brain metastasis model. Additionally, RNA sequencing revealed several uniquely expressed genes and significantly enriched genes related to tissue development, cell death, and cell migration tumors treated with anti-CD47 antibodies. Thus, demonstrating that CD47 blockade affects cancer cell and tumor microenvironment signaling to limit metastatic spread and may be an effective therapeutic for triple-negative breast cancer brain metastasis.

cancer biology↗

Non-cell autonomous cardiomyocyte regulation complicates gene supplementation therapy for LMNA cardiomyopathy

AimsRecombinant adeno-associated viruses (rAAVs) are federally approved gene delivery vectors for in vivo gene supplementation therapy. Loss-of-function truncating variants of LMNA, the coding gene for Lamin-A/C, are one of the primary causes of inherited dilate cardiomyopathy (DCM). Here we aim to study whether AAV-based LMNA supplementation could treat LMNA deficiency-triggered cardiac defects. Methods and ResultsWe compared whole-body, cardiomyocyte-specific and genetic-mosaic mouse models that carry Lmna truncating variants at the same genetic loci and uncovered primarily a non-cell autonomous impact of Lmna on cardiomyocyte maturation. Whole-body lamin-A supplementation by rAAVs moderately rescued the cardiac defects in Lmna germline mutants. By contrast, cardiomyocyte-specific lamin-A addback failed to restore the cardiomyocyte growth defects. A Cre-loxP-based AAV vector that expresses lamin-A throughout the body but excluding the heart was able to restore cardiomyocyte growth in Lmna germline mutants. ConclusionsLmna regulates cardiomyocyte growth non-cell autonomously. Non-myocytes are the key cell targets for a successful gene therapy for LMNA-associated cardiac defects. Translational perspectiveLMNA truncating mutations are among the major causes of inherited DCM. AAV gene supplementation therapy is emerging as a promising strategy to treat genetic cardiomyopathy, but whether this strategy is suitable for LMNA cardiomyopathy remained unclear. Our study counterintuitively showed that the cardiomyocytes are not necessarily the correct therapeutic cell targets for AAV-based treatment of LMNA cardiomyopathy. By contrast, careful elucidation of cell-autonomous versus non-cell-autonomous gene functions is essential for the proper design of a gene supplementation therapy for cardiomyopathy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/549413v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@37cfdaorg.highwire.dtl.DTLVardef@2f2cd1org.highwire.dtl.DTLVardef@1278d08org.highwire.dtl.DTLVardef@19c4869_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Inferring Neuron-level Brain Circuit Connection via Graph Neural Network Amidst Small Established Connections

MotivationReconstructing neuron-level brain circuit network is a universally recognized formidable task. A significant impediment involves discerning the intricate interconnections among multitudinous neurons in a complex brain network. However, the majority of current methodologies only rely on learning local visual synapse features while neglecting the incorporation of comprehensive global topological connectivity information. In this paper, we consider the perspective of network connectivity and introduce graph neural networks to learn the topological features of brain networks. As a result, we propose Neuronal Circuit Prediction Network (NCPNet), a simple and effective model to jointly learn node structural representation and neighborhood representation, constructing neuronal connection pair feature for inferring neuron-level connections in a brain circuit network. ResultsWe use a small number of connections randomly selected from a single brain circuit network as training data, expecting NCPNet to extrapolate known connections to unseen instances. We evaluated our model on Drosophila connectome and C. elegans worm connectome. The numerical results demonstrate that our model achieves a prediction accuracy of 91.88% for neuronal connections in the Drosophila connectome when utilizing only 5% of known connections. Similarly, under the condition of 5% known connections in C. elegans, our model achieves an accuracy of 93.79%. Additional qualitative analysis conducted on the learned representation vectors of Kenyon cells indicates that NCPNet successfully acquires meaningful features that enable the discrimination of neuronal sub-types. Our project is available at https://github.com/mxz12119/NCPNet.

neuroscience↗

ZBP1-mediated macrophage necroptosis inhibits ASFV replication

African swine fever (ASF) is an infectious disease characterized by hemorrhagic fever, highly pathogenic, and severe mortality in domestic pigs caused by the African swine fever virus (ASFV). ASFV is a large DNA virus and primarily infects porcine monocyte macrophages. The interaction between ASFV and host macrophages is the major reason for gross pathological lesions caused by ASFV. Necroptosis is an inflammatory programmed cell death and plays an important immune role during virus infection. However, whether and how ASFV induces macrophage necroptosis and what effect of necroptosis signaling on host immunity and ASFV infection remains unknown. This study uncovered that ASFV activates the necroptosis signaling in the spleen, lung, liver, and kidney from ASFV-infected pigs. And macrophage necroptosis also was induced by ASFV infection in vitro. Further evidence showed that the macrophage necroptosis is independent of TNF--RIPK1 or TLR-TRIF pathway but depends on Z-DNA binding protein 1 (ZBP1). ASFV infection upregulates the expression of ZBP1 and RIPK3 to consist of the ZBP1-RIPK3-MLKL necrosome and further activates macrophage necroptosis. Subsequently, multiple Z-DNA sequences were predicted to be present in the ASFV genome. And the Z-DNA signals were further confirmed to be present and colocalized with ZBP1 in the cytoplasm and nucleus of ASFV-infected cells. Moreover, ZBP1-mediated macrophage necroptosis caused the extracellular release of proinflammatory cytokines TNF- and IL-1{beta} induced by ASFV infection. Finally, we demonstrated that ZBP1-mediated necroptosis signaling significantly inhibits ASFV replication in host macrophages. Our findings uncovered a novel mechanism by which ASFV induces macrophage necroptosis by facilitating Z-DNA accumulation and ZBP1 necrosome assembly, providing significant insights into the pathogenesis of ASFV infection. ImportanceASFV infection causes an acute, febrile, hemorrhagic, and severely lethal disease in swine, which seriously threatens the global porcine industry. Understanding the interaction mechanism between ASFV and host macrophages during infection is essential for elucidating the pathogenesis of ASFV. To our knowledge, this study revealed the interaction mechanism between ASFV infection and host macrophage necroptosis. The results showed that ASFV infection induces macrophage necroptosis through ZBP1 activation instead of the TNF--RIPK1 or TLR-TRIF pathway. ASFV infection promotes Z-DNA accumulation, which causes ZBP1-RIPK3-MLKL necrosome assembly and macrophage necroptosis. The ZBP1-mediated necroptosis signaling facilitates the extracellular release of proinflammatory cytokines, inhibiting ASFV replication in host macrophages. This study found a new interaction mechanism between ASFV and host macrophages, which may help understand the pathogenesis caused by ASFV infection.

microbiology↗

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. By analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiome. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes (MAGs), which represent 1897 species spanning 106 phyla. In addition, beta diversity analysis indicates that both sampling site and cold seep type have substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, indicating the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences encode potentially novel natural products. These natural products are dominated by ribosomal processing peptides, which are widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource which would enhance the understanding and utilization of global cold seep microbiomes.

microbiology↗

Tat-fimbriae ("tafi") - novel type of haloarchaeal surface structures

In present study, we describe "tat-fimbriae (tafi)" - a novel type of archaeal surface appendages isolated from haloarchaeon Haloarcula hispanica. These filamental structures are unique because they are formed of protein subunits secreted through the twin-arginine translocation pathway (Tat-pathway), in contrast to well-known archaeal surface filamentous structures secreted by the general secretory pathway (Sec-pathway). No cases of the role of Tat-pathway in the assembly of archaeal and bacterial filamentous structures have been described to date. "Tafi" are the first example of such structures. The precursor of the major tafi protein subunit TafA contains the N-terminal signal peptide carrying a twin-arginine consensus motif and fimbria-forming mature TafA lacks this signal peptide. We analyzed the gene neighborhood of the tafA homologues in the known haloarchaeal genomes and found a conservative cluster of seven associated genes tafA, B, C, D, E, F, G. We assume that all of them take part in the tafi synthesis. TafC and TafE proteins, whose precursor sequences also contain twin-arginine motifs, were detected as minor components of tafi. TafE protein is structurally similar to TafA, while TafC contains a TafA-like N-terminal domain and a C-terminal "laminin G-like" domain capable of functioning as an adhesin. TafD is annotated as a signal peptidase I. The functions of TafB, TafF and TafG are not known yet. This study demonstrated that {Delta}tafA and {Delta}tafD deletion mutant strains synthesized archaella and not tafi, and only tafi were detected in {Delta}arlK (gene of common archaellin/pilin signal peptidase) deletion strain. It was shown that the expression of complete Har. hispanica taf-gene cluster in a heterologous host Haloferax volcanii that does not have similar genes leads to synthesis of recombinant tafi structures similar to the native ones. The tafi function remains elusive, but our preliminary data suggest that these structures may be involved in cell adhesion to different surfaces or substrates.

microbiology↗

High fat diet ameliorates the mitochondrial cardiomyopathy of CHCHD10 mutant mice

Mutations in CHCHD10, a mitochondrial protein with undefined functions, are associated with autosomal dominant mitochondrial diseases. Chchd10 knock-in mice harboring a heterozygous S55L mutation (equivalent to human pathogenic S59L) develop a fatal mitochondrial cardiomyopathy caused by CHCHD10 aggregation and proteotoxic mitochondrial integrated stress response (mtISR). In mutant hearts, mtISR is accompanied by a metabolic rewiring characterized by increased reliance on glycolysis rather than fatty acid oxidation. To counteract this metabolic rewiring, heterozygous S55L mice were subjected to chronic high fat diet (HFD) to decrease insulin sensitivity and glucose uptake and enhance fatty acid utilization in the heart. HFD ameliorated the ventricular dysfunction of mutant hearts and significantly extended the survival of mutant female mice affected by severe pregnancy-induced cardiomyopathy. Gene expression profiles confirmed that HFD increased fatty acid utilization and ameliorated cardiomyopathy markers. Importantly, HFD also decreased accumulation of aggregated CHCHD10 in the S55L heart, suggesting activation of quality control mechanisms. Overall, our findings indicate that metabolic therapy can be effective in mitochondrial cardiomyopathies associated with proteotoxic stress.

molecular biology↗