High-resolution view at the coding transcriptome and noncoding RNAs of major gut microbe Bacteroides thetaiotaomicron

Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). Our screen identified ~4,500 TSSs and we globally determined untranslated regions (UTRs), operon structures, and promoter motifs. In addition, dRNA-seq led to the discovery of ~250 noncoding RNA elements, including 124 novel intergenic small RNAs (sRNAs), several of which we validated experimentally. One of them is the conserved, 145 nt-long sRNA BTnc035, that was highly expressed when B. thetaiotaomicron was grown in the presence of N-acetylglucosamine or glucuronic acid as the sole carbon source. Combining computational predictions with experimental data, we determined the secondary structure of BTnc035 and identified target genes of this sRNA. The emerging model places BTnc035 at the center of a metabolic feedback-loop, wherein sensing of N-acetyl-D-glucosamine and D-glucuronic acid induces BTnc035, which in turn may contribute to a metabolic switch from polysaccharide biosynthesis to break-down. Together, we compiled a single-nucleotide resolution transcriptome map of B. thetaiotaomicron and provide the first global analysis of noncoding RNAs in this important anaerobic model bacterium. To allow easy interrogation of our transcriptome data, we developed Theta-Base – an intuitive online browser that can be freely accessed at https://www.helmholtz-hiri.de/en/bacteroides. Overall design: Samples 1-18: Genome-wide mapping of transcription start sites via differential RNA-seq (dRNA-seq) of Bacteroides thetaiotaomicron VPI-5482 (wild type) grown in TYG to early-logarithmic phase (ELP), mid-logarithmic phase (MLP) and stationary phase (stat). Three biological replicates per strain and condition. Samples 19-24: Comparative expression analysis by RNA-seq of B. thetaiotaomicron wild-type (tdk deletion background), ?BTnc035 (BTnc035 deletion mutant), and BTnc035+ (BTnc035 complementation strain). Two biological replicates per strain.