A phage-encoded GapR nucleoid-associated protein binds a bacterial GapR to deactivate it via an inhibitory hetero-oligomer mechanism

Nucleoid-associated proteins (NAPs) play key roles in bacterial chromosome organization and cellular processes. Recent work identified GapR as an essential NAP that is ubiquitous in α-proteobacteria. GapR structures revealed that the GapR dimer can form dimer of dimers in the presence of DNA to create a DNA-encasing clamp and data showed that GapR is required for bacterial replication as it recruits topoisomerases to regions of overtwisted DNA. Interestingly, diverse phages that infect α-proteobacteria encode GapR homologs. To gain insight into how phage GapRs may impact their cellular homologs we performed structure/function analyses on the Roseobacterial and Roseophage RDJLΦ1 GapR proteins. Crystal structures revealed that the RDJLΦ1 GapR structure differs from that of the bacterial GapR in a way that is incompatible with DNA binding. Cellular localization and fluorescence binding assays confirmed that the RDJLΦ1 phage GapR does not bind DNA. Strikingly, we show that the RDJLΦ1 GapR and Roseobacterial GapR can form heterodimers that are unable to bind DNA, suggesting the phage GapR may act as a bacterial GapR poison. This was further supported by cellular studies. Collectively these studies reveal a unique autoinhibitory mechanism by which a phage encoded NAP impacts DNA binding by the host NAP.