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Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. Working with bacterial mRNA is challenging because it lacks a poly(A)‐tail. However, methods for detecting RNA modifications, both sequencing and mass spectromet...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9542048/ https://www.ncbi.nlm.nih.gov/pubmed/35822398 http://dx.doi.org/10.1002/cbic.202200270 |
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author | Petrov, Dimitar Plamenov Kaiser, Steffen Kaiser, Stefanie Jung, Kirsten |
author_facet | Petrov, Dimitar Plamenov Kaiser, Steffen Kaiser, Stefanie Jung, Kirsten |
author_sort | Petrov, Dimitar Plamenov |
collection | PubMed |
description | mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. Working with bacterial mRNA is challenging because it lacks a poly(A)‐tail. However, methods for detecting RNA modifications, both sequencing and mass spectrometry, rely on efficient preparation of mRNA. Here, we compared size‐dependent separation by electrophoresis and rRNA depletion for enrichment of Escherichia coli mRNA. The purification success was monitored by qRT‐PCR and RNA sequencing. Neither method allowed complete removal of rRNA. Nevertheless, we were able to quantitatively analyze several modified nucleosides in the different RNA types. We found evidence for stress dependent RNA modification reprofiling in rRNA, but also several modified nucleosides in the mRNA enriched fractions showed significant changes. |
format | Online Article Text |
id | pubmed-9542048 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95420482022-10-14 Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli Petrov, Dimitar Plamenov Kaiser, Steffen Kaiser, Stefanie Jung, Kirsten Chembiochem Research Articles mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. Working with bacterial mRNA is challenging because it lacks a poly(A)‐tail. However, methods for detecting RNA modifications, both sequencing and mass spectrometry, rely on efficient preparation of mRNA. Here, we compared size‐dependent separation by electrophoresis and rRNA depletion for enrichment of Escherichia coli mRNA. The purification success was monitored by qRT‐PCR and RNA sequencing. Neither method allowed complete removal of rRNA. Nevertheless, we were able to quantitatively analyze several modified nucleosides in the different RNA types. We found evidence for stress dependent RNA modification reprofiling in rRNA, but also several modified nucleosides in the mRNA enriched fractions showed significant changes. John Wiley and Sons Inc. 2022-07-29 2022-09-16 /pmc/articles/PMC9542048/ /pubmed/35822398 http://dx.doi.org/10.1002/cbic.202200270 Text en © 2022 The Authors. ChemBioChem published by Wiley-VCH GmbH https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Petrov, Dimitar Plamenov Kaiser, Steffen Kaiser, Stefanie Jung, Kirsten Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli |
title | Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
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title_full | Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
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title_fullStr | Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
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title_full_unstemmed | Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
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title_short | Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
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title_sort | opportunities and challenges to profile mrna modifications in escherichia coli |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9542048/ https://www.ncbi.nlm.nih.gov/pubmed/35822398 http://dx.doi.org/10.1002/cbic.202200270 |
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