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RNA degradation analysis reveals ribosome dynamics in complex microbiome samples

View ORCID ProfileSusanne Huch, View ORCID ProfileLilit Nersisyan, Maria Ropat, View ORCID ProfileDonal Barret, Jing Wang, View ORCID ProfileJaime Huerta-Cepas, View ORCID ProfileWu Wei, View ORCID ProfileLars M Steinmetz, View ORCID ProfileLars Engstrand, View ORCID ProfileVicent Pelechano
doi: https://doi.org/10.1101/2021.04.08.439066
Susanne Huch
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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  • ORCID record for Susanne Huch
Lilit Nersisyan
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Maria Ropat
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Donal Barret
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Jing Wang
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Jaime Huerta-Cepas
2Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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Wu Wei
3Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Lars M Steinmetz
4Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
5Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
6European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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Lars Engstrand
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Vicent Pelechano
1SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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  • For correspondence: vicente.pelechano.garcia@ki.se
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Abstract

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 Statement

VP has filed a patent application regarding part of the work described in this manuscript.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 10, 2021.
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RNA degradation analysis reveals ribosome dynamics in complex microbiome samples
Susanne Huch, Lilit Nersisyan, Maria Ropat, Donal Barret, Jing Wang, Jaime Huerta-Cepas, Wu Wei, Lars M Steinmetz, Lars Engstrand, Vicent Pelechano
bioRxiv 2021.04.08.439066; doi: https://doi.org/10.1101/2021.04.08.439066
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RNA degradation analysis reveals ribosome dynamics in complex microbiome samples
Susanne Huch, Lilit Nersisyan, Maria Ropat, Donal Barret, Jing Wang, Jaime Huerta-Cepas, Wu Wei, Lars M Steinmetz, Lars Engstrand, Vicent Pelechano
bioRxiv 2021.04.08.439066; doi: https://doi.org/10.1101/2021.04.08.439066

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