RNA degradation analysis reveals ribosome dynamics in complex microbiome samples

ABSTRACT: The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. Here we demonstrate that, contrary to expectation, co-translational mRNA degradation is common in prokaryotes, and that in vivo ribosome protection generates widespread 3-nt periodicity in 5´P mRNA decay intermediates. Consequently, 5´P sequencing allows the study of codon and gene specific ribosome stalling in response to stress and drug treatment at single nucleotide resolution. We validate its wide applicability by investigating in vivo species-specific ribosome footprints of clinical and environmental microbiomes and show that amino acid-specific ribosome protection patterns can be used to phenotype microbiome perturbations. Furthermore, we show that multiple RNase activities collaborate to generate in vivo ribosome footprints and that co-translational degradation is phylogenetically conserved across prokaryotes. This strategy opens the way for the study of the metatranslatome, and allows to investigate fast species-specific post-transcriptional responses to environmental and chemical perturbations in unculturable microbial communities.

ORGANISM(S): Segatella copri Escherichia coli Hoylesella timonensis Lactiplantibacillus plantarum Saccharomyces cerevisiae Limosilactobacillus fermentum Listeria monocytogenes Enterococcus faecalis Bacillus subtilis Salmonella enterica Synechocystis sp. PCC 6803 Alistipes finegoldii Bacillus amyloliquefaciens Cryptococcus neoformans Caulobacter vibrioides human feces metagenome Staphylococcus aureus compost metagenome Limosilactobacillus reuteri Parabacteroides merdae

PROVIDER: GSE153497 | GEO | 2023/03/24

REPOSITORIES: GEO