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Updated: Sep 5, 2025

Quantification of the Abundance and Charging Levels of Transfer RNAs in Escherichia coli
Published on: August 22, 2017
Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli
Dimitar Plamenov Petrov1, Steffen Kaiser2,3, Stefanie Kaiser2,3
1Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany.
Abstract:
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.
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