Because gene expression is crucial for normal development, all organisms have multiple mechanisms to ensure that the correct genes are expressed at the correct time. Many of these mechanisms occur during transcription, the process of transcribing DNA into RNA. We study the regulation of transcription in very simple cells as model systems for understanding how this process is regulated at a molecular level. Our work has identified proteins and DNA sequences that play key roles in the expression of virulence genes in Bordetella pertussis, the causative agent of whooping cough. We have also found similar proteins and DNA sequences that play key roles in the body’s ability to promote or inhibit its defense against a virus that infects E. coli bacterium. Our work provides insight into how similar processes work in higher organisms and may reveal new antibacterial strategies.