A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.
Daniel RyanLaura JennichesSarah ReichardtLars BarquistAlexander J WestermannPublished in: Nature communications (2020)
Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called 'Theta-Base' ( www.helmholtz-hiri.de/en/datasets/bacteroides ), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N-acetyl-D-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes.
Keyphrases
- rna seq
- genome wide
- single cell
- gene expression
- high resolution
- dna methylation
- electronic health record
- endothelial cells
- poor prognosis
- transcription factor
- big data
- nucleic acid
- working memory
- mass spectrometry
- machine learning
- living cells
- fluorescent probe
- transcranial magnetic stimulation
- pluripotent stem cells
- data analysis
- sensitive detection
- prefrontal cortex
- long non coding rna
- deep learning
- high speed
- genetic diversity