Temporal Regulation of Viral Transcription during Development of Thermus thermophilus Bacteriophage ϕYS40

Abstract Regulation of gene expression of lytic bacteriophage ϕYS40 that infects the thermophilic bacterium Thermus thermophilus was investigated and three temporal classes of phage genes, early, middle, and late, were revealed. ϕYS40 does not encode a (RNAP) and must rely on host RNAP for transcription of its genes. Bioinformatic analysis using a model of Thermus promoters predicted 43 putative σ A -dependent −10/−35 class phage promoters. A randomly chosen subset of those promoters was shown to be functional in vivo and in vitro and to belong to the early temporal class. Macroarray analysis, primer extension, and bioinformatic predictions identified 36 viral middle and late promoters. These promoters have a single common consensus element, which resembles host σ A RNAP holoenzyme –10 promoter consensus element sequence. The mechanism responsible for the temporal control of the three classes of promoters remains unknown, since host σ A RNAP holoenzyme purified from either infected or uninfected cells efficiently transcribed all ϕYS40 promoters in vitro . Interestingly, our data showed that during infection, there is a significant increase and decreaseof transcript amounts of host translation initiation factors IF2 and IF3, respectively. This finding, together with the fact that most middle and late ϕYS40 transcripts were found to be leaderless, suggests that the shift to late viral gene expression may also occur at the level of mRNA translation.