Beyond AMGs: Phage-encoded transcription and sigma factors as understudied virocell reprogramming tools

Phages, the most abundant biological entities on Earth, infect bacteria and reprogram them into 'virocells' with altered physiology and ecology. While metagenomic studies have largely inferred reprogramming through virus-encoded auxiliary metabolic genes (AMGs), phages can reprogram cells through many other tools. In this review, we explore how phage-encoded, host-acting transcription and sigma factors (TSFs) reshape host transcriptional networks beyond simply regulating phage replication. We synthesize emerging genomic evidence for TSF prevalence in phages, mechanistic insights into how host-acting TSFs might influence ecologically relevant cellular functions, and highlight recent experimental and bioinformatic advances that make TSFs particularly tractable for large-scale bioinformatic studies. Together, we position TSFs as AMG-complementary mechanisms of viral reprogramming, tractable for metagenomic inferences, with potential cellular- and ecosystem-level consequences that can power translational applications.