Mycobacteriophage Cluster A Immunity Repressors: A Conserved Protein Fold Adapted for Diverse Biological Functions

Abstract Mycobacteriophage cluster A immunity repressors are unusual in that they silence lytic gene expression by binding numerous DNA binding sites located throughout the viral genome. They can also provide immunity to infection by genetically similar phages that contain the same or similar DNA binding sites. Despite containing similar DNA binding sites and repressor proteins, cluster A viruses often display heteroimmune phenotypes, the molecular details of which are currently unclear. Using a combination of small-angle X-ray scattering, protein crystallography, bioinformatics, and DNA binding and in vivo immunity assays, we show that cluster A repressors conserve a common protein fold yet appear to provide DNA specificity through a narrow region of the novel stoperator DNA binding domain. Additionally, both viral and bacterial genomes contain cluster A-like repressor proteins fused to diverse protein domains, which suggest that these repressors have evolved to do more than just silence viral lytic gene expression.