Aquatic metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA261440 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Biodegradation of organic micropollutants in GAC filters – temporal development and spatial variations
| PRJEB71093 | ENA
Project description:The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear.IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
| S-EPMC7029224 | biostudies-literature
Project description:Context: Ginkgolic acid (GAC), one of the major active constituents of Ginkgo biloba L. (Ginkgoaceae) extract, has been reported as a potential anticancer drugs. Objective: To investigate the effect of GAC on the viability of Human hepatocellular carcinoma (HCC) cells and its underlying mechanisms. Materials and methods: Human HCC cell lines and an orthotopic HCC mouse model were employed. RNA sequencing, drug affinity responsive target stability (DARTS) with LC-MS/MS, protein–protein interaction analysis, molecular docking, and cellular thermal shift assay (CETSA) were used to identify and validate GAC targets. Ferroptosis was evaluated by BODIPY probes, Annexin-V/PI staining, Western blotting, malondialdehyde (MDA), GSH/GSSG assays, and transmission electron microscopy (TEM). Cell viability was assessed by CCK-8 and colony formation assays. HSPA8 knockdown, mutant, and KFERQ-reporter cells were generated to investigate the role of HSPA8 and chaperone-mediated autophagy (CMA). Results: GAC effectively inhibits the viability of HCC by triggering ferroptosis. HSPA8 was identified as the directly target of GAC. The binding of GAC with HSPA8 enhancing its interaction with glutathione peroxidase 4 (GPX4), which leads to the degradation of GPX4 via CMA. This process depleted glutathione (GSH) and caused lipid peroxidation, finally inducing ferroptosis in HCC cells. Furthermore, GAC suppressed tumor growth in an orthotopic HCC model, increased lipid peroxidation and GPX4 degradation in tumor tissues. Discussion and conclusions: Our results revealed a novel mechanism by which GAC induces ferroptosis in HCC cells through direct targeting HSPA8 and promoting CMA-dependent GPX4 degradation. These findings demonstrate the potential of GAC as therapeutic approaches for HCC.
2026-04-01 | GSE317008 | GEO
Project description:The gene GLS generates the phosphate activated glutaminase C (GAC) isoform by alternative splicing. GAC, compared to the other isoform, kidney-type glutaminase (KGA), has been characterized as more active and particularly important for cancer cell growth. Very little is known about post-translational modifications regulating GAC function. Hereby we describe the identification of a phosphorylation on the serine 95, located at the GLS N-terminus, a domain shared by both isoforms. A GAC phosphomimetic mutant (S95D) ectopically expressed in breast cancer cells presented decreased enzymatic activity, and its expression impacted on cell’s glutamine uptake, glutamate release and intracellular glutamate levels (compared to expressing wild type GAC) without changing GAC sub-cellular localization. Curiously, replacing S95 by an alanine in the ectopically expressed GAC (S95A) increased cell proliferation and migration. Taken together, these results reveal that GAC is post-translationally regulated by phosphorylation, which impacts on cancer phenotype.
2018-08-13 | PXD008338 | Pride
Project description:We identified several hub genes and key pathways associated with GAC initiation and progression by analysising the microarray data on DEGs, whcih provided a detailed molecular mechanism underlying GAC occurrence and progression.
2019-06-10 | GSE118916 | GEO
Project description:Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 at lysine 22 (rpL40K22me3) by the lysine methyltransferase (KMT) SMYD5 regulates mRNA translation output to promote gastric adenocarcinoma (GAC) malignant progression with lethal peritoneal ascites. A biochemical-proteomic strategy identifies the mono-ubiquitin fusion protein partner rpL40 as the principal physiologic substrate of SMYD5 across diverse samples. Inhibiting the SMYD5-rpL40K22me3 axis in GAC cell lines reprograms protein synthesis to attenuate oncogenic gene expression signatures. SMYD5 and rpL40K22me3 are upregulated in GAC patient samples and negatively correlate with clinical outcomes. SMYD5 ablation in vivo in familial and sporadic mouse models of malignant GAC blocks metastatic disease including peritoneal carcinomatosis (PC). Suppressing SMYD5 methylation of rpL40 inhibits human cancer cell and patient-derived GAC xenograft growth and renders them hypersensitive to PI3K/mTOR inhibitors. Finally, combining SMYD5 depletion with PI3K/mTOR inhibition and CAR-T administration cures an otherwise lethal in vivo mouse model of aggressive GAC-derived PC. Together, our work uncovers a ribosome-based epigenetic mechanism that facilitates evolution of malignant GAC and nominates SMYD5 targeting as part of a potential cornerstone combination therapy to treat a deadly cancer.
2024-03-01 | GSE238257 | GEO
Project description:We developed an extraction-free qPCR assay to identify Omicron BA.1 cases and verified lineage by sequencing. We find that BA.2 variants show almost twice the viral load (Ct) compared to both BA.1 as well as Delta variants.
2022-05-25 | E-MTAB-11650 | biostudies-arrayexpress
Project description:The phylum of Apicomplexa groups intracellular parasites that employ substrate-dependent gliding motility to invade host cells, egress from the infected cells and cross biological barriers. The glideosome associated connector (GAC) is a conserved protein essential to this process. GAC facilitates the association of actin filaments with surface transmembrane adhesins and the efficient transmission of the force generated by myosin translocation of actin to the cell surface substrate. Here, we present the crystal structure of Toxoplasma gondii GAC and reveal a unique, supercoiled armadillo repeat region that adopts a closed ring conformation. Characterisation of the membrane binding interface within the C-terminal PH domain as well as an N-terminal fragment necessary for association with F-actin suggest that GAC adopts multiple conformations. A multi-conformational model for assembly of GAC within the glideosome is proposed
2023-05-10 | PXD039335 | Pride