Quantitative analysis of a virulent bacteriophage transcription strategy

An increasingly large number of bacteriophage genomes are being sequenced each year. What is an efficient experimental and computational procedure to analyze transcription strategies of newly sequenced novel bacteriophages? We address this issue using an example of bacteriophage Xp10, which infects rice pathogen Xanthomonas oryzae. This phage is particularly challenging for analysis, since part of its genome is jointly transcribed by two (host and viral) RNA polymerases. To understand the roles played by the two RNA polymerases, we developed a novel method of data analysis which combines quantitative analysis of Xp10 global gene expression data and kinetic modeling of the infection process. To generalize our approach, we discuss how our method can be applied to other systems and argue that genomic array experiments combined with the methods of data analysis that we present provide an efficient way to analyze gene expression strategies of novel bacteriophages.