title: Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases.
abstract: Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, phiA1122, T3, phiYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used to scan the corresponding genomes, a significant gap in the individual information distribution was observed between functional promoter sites and other sequences, suggesting that the models can be used to identify new T7-like promoters. When a combined 76-site model was used to scan the eight phages, 108 of the total 109 promoters were found, while none were found for other T7-like phages, phiKMV, P60, VpV262, SIO1, PaP3, Xp10, P-SSP7 and Ppu40, indicating that these phages do not belong to the T7 group. We propose that the T7-like transcription system, which consists of a phage-specific RNA polymerase and a set of conserved T7-like promoters, is a hallmark feature of the T7 group and can be used to classify T7-like phages. Phylogenetic trees of the T7-like promoter models and their corresponding RNA polymerases are similar, suggesting that the eight phages of the T7 group can be classified into five subgroups. However the SP6-like polymerases have apparently diverged from other polymerases more than their promoters have diverged from other promoters.
authors.affiliation: Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA.
authors.forename: Zehua
authors.initials: Z
authors.lastname: Chen
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Schneider
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D023281:Genomics; D007257:Information Theory; D008957:Models, Genetic; D010802:Phylogeny; D017902:Podoviridae / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014764:Viral Proteins / Q000145:classification* / Q000235:genetics
chemical_list: D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases