T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of 
Escherichia coli during infection through a phage-encoded decapping enzyme

Wolfram-Schauerte, Maik; Moskalchuk, Anastassiya; Pozhydaieva, Nadiia; Ramírez Rojas, Adán Andrés; Schindler, Daniel; Kaiser, Stefanie; Paczia, Nicole; Höfer, Katharina

doi:10.1101/2024.04.04.588121

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T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme

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Wolfram-Schauerte, Maik
Max Planck Research Group Bacterial Epitranscriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Moskalchuk, Anastassiya
Max Planck Research Group Bacterial Epitranscriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Pozhydaieva, Nadiia
Max Planck Research Group Bacterial Epitranscriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Ramírez Rojas, Adán Andrés
Core Facility MPG MAXGenesys DNAfoundry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Schindler, Daniel
Core Facility MPG MAXGenesys DNAfoundry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Paczia, Nicole
Core Facility Metabolomics and small Molecules Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Höfer, Katharina
Max Planck Research Group Bacterial Epitranscriptomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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https://doi.org/10.1101/2024.04.04.588121
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Citation

Wolfram-Schauerte, M., Moskalchuk, A., Pozhydaieva, N., Ramírez Rojas, A. A., Schindler, D., Kaiser, S., et al. (2024). T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme. bioRxiv: the preprint server for biology, 2024.04.04.588121.

Cite as: https://hdl.handle.net/21.11116/0000-000F-1FE8-A

Abstract

Nicotinamide adenine dinucleotide (NAD) serves as a cap-like structure on cellular RNAs (NAD-RNAs) in all domains of life including the bacterium Escherichia coli. NAD also acts as a key molecule in phage-host interactions, where bacterial immune systems deplete NAD to abort phage infection. Nevertheless, NAD-RNAs have not yet been identified during phage infections of bacteria and the mechanisms of their synthesis and degradation are unknown in this context. The T4 phage that specifically infects E. coli presents an important model to study phage infections, but a systematic analysis of the presence and dynamics of NAD-RNAs during T4 phage infection is lacking. Here, we investigate the presence of NAD-RNAs during T4 phage infection in a dual manner. By applying time resolved NAD captureSeq, we identify NAD-capped host and phage transcripts and their dynamic regulation during phage infection. We provide evidence that NAD-RNAs are