Ontology highlight
ABSTRACT:
PROVIDER: PRJNA419203 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:bgc-gene-product model is a Named Entity Recognition (NER) model that identifies and annotates the protein products of Biosynthetic Gene Clusters (BGCs) in texts.
2022-03-10 | MODEL2203040006 | BioModels
Project description:Interventions: Ten subjects receive probiotic product contained 10 million CFU in viable form 3 times a day for 6 months,Ten subjects receive probiotic product contained 10 million CFU in non viable form 3 times a day for 6 months, Ten subjects receive product without probiotic 3 times a day for 6 months;Active Comparator Dietary Supplement,Active Comparator Dietary Supplement,Placebo Comparator Dietary Supplement;probiotic products in viable form,probiotic products in non viable form,Control
Primary outcome(s): reduceing of number of pathogens in gut at 6 months after intervention number of pathogens / Anova
Study Design: Randomized
| 2727906 | ecrin-mdr-crc
Project description:Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora
2016-01-27 | MSV000079484 | GNPS
Project description:CD4+ T helper 17 (Th17) cells protect vertebrate hosts from extracellular pathogens at mucosal surfaces. Th17 cells form from naïve precursors when signals from the T cell antigen receptor (TCR) and certain cytokine receptors induce the expression of the RORγt transcription factor, which activates a set of Th17-specific genes. Using T cell-specific loss-of-function experiments we find that two components of the Polycomb Repressive Complex 1.1 (PRC1.1), BCL6 corepressor (BCOR) and KDM2B, which helps target the complex to unmethylated CpG DNA islands, are required for optimal Th17 cell formation in mice after Streptococcus pyogenes infection. Genome-wide expression and BCOR chromatin immunoprecipitation studies revealed that BCOR directly represses Lef1, Runx2, and Dusp4, whose products inhibit Th17 differentiation. Together, the results suggest that PRC1.1 components, BCOR and KDM2B, work together to enhance Th17 cell formation by repressing Th17 fate suppressors.
2019-04-26 | GSE121766 | GEO
Project description:<p>Natural products from microorganisms are important sources for drug discovery. With the development of high-throughput sequencing technology and bioinformatics, a large amount of uncharacterized biosynthetic gene clusters (BGCs) in microorganisms have been found, which show the potential for novel natural product production. 9 BGCs containing PKS and/or NRPS in <em>Streptomyces globisporus</em> C-1027 were transcriptionally low/silent under the experimental fermentation conditions, and the products of these clusters are unknown. Thus, we tried to activate these BGCs to explore cryptic products of this strain. We constructed the cluster-situated regulator overexpressing strains which contained regulator gene(s) under the control of the constitutive promoter <em>ermE</em>*p in <em>S. globisporus</em> C-1027. Overexpression of regulators in cluster 26 resulted in significant transcriptional upregulation of biosynthetic genes. With the separation and identification of products from the overexpressing strain OELuxR1R2, 3 <em>ortho</em>-methyl phenyl alkenoic acids (compounds <strong>1-3</strong>) were obtained. Gene disruption showed that compounds <strong>1</strong> and <strong>2</strong> were completely abolished in the mutant GlaEKO, but were hardly affected by deletion of the genes <em>orf3</em> or <em>echA</em> in cluster 26. The type II PKS biosynthetic pathway of chain-extended cinnamoyl compounds was deduced by bioinformatics analysis. This study showed that overexpression of the 2 adjacent cluster-situated LuxR regulator(s) is an effective strategy to connect the orphan BGC to its products.</p>
2023-09-06 | MTBLS5152 | MetaboLights
Project description:Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was described about 100 years ago as the causative agent of Bakanae (M-bM-^@M-^\foolish seedlingM-bM-^@M-^]) disease of rice. Apart from GAs, the fungus is known to produce pigments and mycotoxins, but the biosynthetic genes are known for only eight products. Here we present a high-quality genome sequence of the first member of the Gibberella fujikuroi species complex (GFC) that allowed de novo genome assembly with 12 scaffolds corresponding to the 12 chromosomes. In this work we focused on identification of all potential secondary metabolism-related gene clusters and their regulation in response to nitrogen availability by transcriptome, proteome, HPLC-FTMS and ChIP-seq analyses. We show that most of the cluster genes are regulated in a nitrogen-dependent manner, and that expression profiles fit to proteome and ChIP-seq data for some but not all clusters. Comparison with genomes of all available Fusarium species, including the recently sequenced F. mangiferae and F. circinatum, showed only a small number of common gene clusters and provides new insights into the divergence of secondary metabolism in the genus Fusarium. Phylogenetic analyses suggest that some gene clusters were acquired by horizontal gene transfer, while others were present in ancient Fusarim species and have evolved differently by gene duplications and losses. One polyketide synthase (PKS) and one non-ribosomal peptide synthetase (NRPS) gene cluster are unique for F. fujikuroi. Their products were identified by combining overexpression of cluster genes with HPLC-FTMS-based analyses. In planta expression studies suggest a specific role of the PKS19 product in rice infection. Our results indicate that comparative genomics together with the used genome-wide experimental approaches is a powerful tool to uncover new secondary metabolites and to understand their regulation at the transcriptional, translational and epigenetic levels. Examination of 3 different histone modifications, with 2 growth conditions for one of the modifications (Total of 4 samples)
2013-10-16 | E-GEOD-46033 | biostudies-arrayexpress
Project description:Lipid extracts from a range of mutants in genes whose gene-products are predicted to localize to the peroxisome were profiled using a 2 minute gradient liquid chromatography method and annotation of lipids based on MS1.
2021-01-28 | MSV000086777 | MassIVE
Project description:Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we hypothesized that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the “coenzyme” category have been examined, including a gene cluster encoding for the co-factor pyrroloquinoline quinone (PQQ). When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides a new engineering strategy for improving polyketide production and discovering new biosynthetic gene clusters.
2024-02-12 | PXD049454 |