A phage-encoded host transcription modulator, Htm, reprograms the transcriptome of ESBL Escherichia coli

Abstract

During phage infection, phages reprogram their host to secure energy, building blocks for their genome, and proteins, as well as the transcription and translation machinery required to replicate their genome and produce phage particles. This also includes reprogramming the host transcriptome to modify host gene expression and align it with the phage’s needs during infection. In this study, we present a putative early-expressed protein, Gp204 of Mosigvirus AV110, renamed Host transcription modulator (Htm), that has a broad impact on the extended-spectrum β-lactamase (ESBL)-associated E. coli transcriptome. Overexpression of Htm decreased the growth rate of ESBL-E. coli and caused DNA condensation. Htm is structurally similar to bacterial enhancer-binding proteins, binds ssDNA, and alters the expression levels of over 700 E. coli genes when expressed. The majority of these genes were upregulated and are involved in multiple pathways, such as galactose metabolism and pentose and glucuronate interconversions, which may promote the synthesis of purines, pyrimidines, and histidine, all of which are required for the replication, transcription, and translation of the phage genome. Furthermore, energy production is likely to be upregulated by increased availability of acetyl-CoA, resulting from, among other factors, fatty acid degradation. Htm also downregulated the expression of the structural genes involved in flagellar assembly and multiple two-component systems. In conclusion, Htm could promote phage progeny production by increasing the availability of nucleotides, amino acids, and energy, while inhibiting non-essential processes, such as flagella formation. Importance Early-expressed proteins have a central role during phage infection by rapidly reprogramming a wide range of host cellular processes. However, the function and impact on the host of many of these proteins remain poorly understood. Investigating these proteins provides fundamental insights into phage-host co-evolution and the mechanisms phages use to support their successful infection and progeny formation. In a broader context, this knowledge may contribute to the development of antimicrobials with a novel mode of action against multidrug-resistant bacteria, such as ESBL E. coli or biotechnological tools to precisely alter bacterial physiology. Our findings indicate that the phage-encoded protein Htm (Host transcription modulator) acts as a regulator of host transcription and demonstrate how early-expressed phage proteins can take control of the host.