RT Journal Article
SR Electronic
T1 RNA degradation analysis reveals ribosome dynamics in complex microbiome samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.08.439066
DO 10.1101/2021.04.08.439066
A1 Susanne Huch
A1 Lilit Nersisyan
A1 Maria Ropat
A1 Donal Barret
A1 Jing Wang
A1 Jaime Huerta-Cepas
A1 Wu Wei
A1 Lars M Steinmetz
A1 Lars Engstrand
A1 Vicent Pelechano
YR 2021
UL http://biorxiv.org/content/early/2021/04/10/2021.04.08.439066.abstract
AB Post-transcriptional regulation is essential for life, yet we are currently unable to investigate its role in complex microbiome samples. Here we discover that co-translational mRNA degradation, where the degradation machinery follows the last translating ribosome, is conserved across prokaryotes. By investigating 5’P mRNA decay intermediates, we obtain in vivo ribosome protection information that allows the study of codon and gene specific ribosome stalling in response to stress and drug treatment at single nucleotide resolution. We use this approach to investigate in vivo species-specific ribosome footprints of clinical and environmental microbiomes and show for the first time that ribosome protection patterns can be used to phenotype microbiome perturbations. Our work paves the way for the study of the metatranslatome, and enables the investigation of fast, species-specific, post-transcriptional responses to environmental and chemical perturbations in unculturable microbial communities.Competing Interest StatementVP has filed a patent application regarding part of the work described in this manuscript.