Project description:Urolithin A is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota which can affect host health. Most, but not all, individuals harbor a microbiota capable of urolithin A production; however, the enzymes that dehydroxylate its dietary precursor, urolithin C, are unknown. Here, we used a combination of transcriptomics and proteomics to reveal a urolithin C dehydroxylase (ucd) operon that dehydroxylates 9-hydroxy urolithin compounds in Enterocloster spp. Using comparative genomics, we identified Lachnoclostridium pacaense as a novel urolithin C metabolizer. Biochemical characterization and structure predictions of proteins in the Ucd complex demonstrated that dehydroxylation was both NADH- and molybdopterin-dependent and used urolithin C as a terminal electron acceptor. A meta-analysis publicly available metagenomic data revealed that both bacteria and ucd operon genes are widely distributed in gut metagenomes and likely comprise keystone species in the metabolism of urolithins by the human gut microbiota.
Project description:To investigate the effects of ppIAPP-GFP expression and urolithin B treatment in the gene expression of Saccharomyces cerevisiae cells, we compared different cells: cells expressing the empty vector, cells expressing ppIAPP-GFP, cells expressing the empty vector treated with urolithin B, cells expressing ppIAPP-GFP treated with urolithin B
Project description:We sought to examine whether urolithin A could alleviate the alcohol-related liver disease. RNA-sequencing (RNA-seq) on mice livers were performed in order to identify the key biological processes and pathways regulated by urolithin A.
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
Project description:To investigate the effect of Uroltihin A on T cell differentiation and gene expression, we treated purified CD3+ cells with DMSO or Urolithin A
