Bacteriophages, viruses that infect bacteria, are promising alternatives to antibiotics in fighting multidrug-resistant infections. However, the advancement of phage therapy is hindered by a lack of understanding regarding the molecular mechanisms underlying bacteriophage-mediated hijacking of host gene expression machinery.
Recent discoveries have underscored the importance of RNA modifications, such as NAD caps, which stabilize RNA transcripts and protect them from degradation by nucleases like RNase E. Our lab has established NAD capture sequencing (NAD captureSeq), a novel technology for identifying and quantifying NAD-capped RNAs, to explore their regulatory functions during phage infection [1].
This study examines the role of Nudix hydrolases in modulating RNA stability in Escherichia coli during T4 phage infection. We hypothesize that while NAD caps may stabilize phage RNA, Nudix hydrolase-mediated decapping could act as a bacterial defense by destabilizing viral RNA and thereby limiting phage replication [2]. By comparing NAD-capped RNA profiles in E. coli strains during infection, we aim to clarify the impact on RNA stability using an integrated approach of NAD captureSeq, transcriptomics, and proteomics.
This project"s outcomes will clarify the role of Nudix-hydrolases in selective RNA decapping during phage infection, providing new insights into how RNA modifications and decapping enzymes contribute to phage-host interactions. Insights from the T4 phage infection model in E. coli will also serve as a valuable framework for exploring phage-host interactions more broadly, informing the design of effective phage therapies against resistant bacterial infections and contributing to efforts addressing global health challenges posed by antibiotic resistance.
[1] Wolfram-Schauerte, M., Moskalchuk, A., Pozhydaieva, N., Ramírez Rojas, A. A., Schindler, D., Kaiser, S., Pazcia, N., & Höfer, K. (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. https://doi.org/10.1101/2024.04.04.588121
[2] Pozhydaieva, N., Wolfram-Schauerte, M., Keuthen, H., & Höfer, K. (2024). The enigmatic epitranscriptome of bacteriophages: putative RNA modifications in viral infections. Current opinion in microbiology, 77, 102417. https://doi.org/10.1016/j.mib.2023.102417