p55, a newly identified Ribbon-Helix-Helix transcription factor encoded by the fusellovirus SSV1: elucidation of an archaeal host-virus relationship

Sulfolobus spindle shaped virus 1 (SSV1) is the type member of the archaeal Fuselloviridae virus family. Viruses belonging to this family share similar features such as genome size, structure and organization as well as viron morphology. The replication of SSV1 has shown to be strongly enhanced by UV-light irradiation. Moreover, the physical map of eleven transcripts (T1-9, Tx and Tind) is available and them transcription patterns have been investigated before and after UV-irradiation of lysogenic cells. Nevertheless, the molecular bases of the viral life cycle induction are still poorly known and unclear. Recently, microarray analyses led to the identification of a twelfth viral transcript, referred as Tp55, which showed high level of expression under condition of no-UV irradiation (carrier stage). This transcript and in turn the encoded protein, named p55, have never been showed to be expressed after UV-light irradiation. In silico analyses of p55 protein sequence have suggested that it could adopt a Ribbon-Helix-Helix fold (RHH), a structural motif typically found in negative transcription regulators. Such kind of regulators has been identified in Bacteria, Archaea and Bacteriophages, but no RHH motifs have been characterized in eukaryotic proteins. Several RHH transcription factors are important for host-pathogen interactions, thus suggesting a convergent evolution of the regulation machineries underlying several unrelated viral life cycles. Unlike the better-characterized Helix-Turn-Helix motif, the DNA-binding-specificity determinants of the RHH motif are located within its amino-terminal -strand. The functional unit of the RHH domain is a twofold symmetric dimer that is capable to bind multiple sites within operons that are arranged as inverted or tandem repeats. Several DNA tandem repeats, that act as targets for p55, have shown to be located in a region of the SSV1 genome critical for the UV-induction. The binding specificity of p55 to these sequences has been tested by band shift assays.