The phage Φ13-encoded transcriptional regulator Ltr controls phage assembly in Staphylococcus aureus

Abstract Background Temperate phages play a central role in the evolution and pathogenicity of Staphylococcus aureus. Sa3int phages provide highly human-specific virulence factors that promote immune evasion and survival within the host. The reversible excision of these phages which occurs without phage production and bacterial lysis allows the simultaneous expression of phage virulence genes and the hlb gene where they usually integrate. However, the regulatory mechanisms that control phage assembly and the cross-talk with host factors remain poorly understood. Methods and results We analyzed the regulatory mechanism controlling late gene transcription of Sa3int phage Φ13. We identified a functional promoter, P23, located upstream of the late phage genes that control DNA processing and packaging, capsid assembly, bacterial lysis and immune evasion. SAOUHSC_02200, the gene located upstream of P23, encodes for a late transcriptional regulator (Ltr). Mutating the P23 TATA-box or the ltr gene abolished P23 activity and formation of mature intact phage particles, thus confirming the role of Ltr in regulating P23 activity. Four direct repeats upstream of the P23 transcriptional start site were identified as potential Ltr binding sites. RT-qPCR analysis confirmed that Ltr-dependent P23 activation is essential for the expression of late genes and the subsequent Φ13 propagation. Furthermore, comparative analysis of P23 activity and ltr expression in different host strain backgrounds revealed strain-specific differences that appear to depend on the alternative sigma factor SigB and its downstream effector SpoVG. Conclusions Ltr controls the expression of late phage genes, thereby regulating phage assembly and lysis. This process is modulated by SpoVG activity.