Thermus thermophilus bacteriophage φYS40 genome and proteomic characterization of virions

We determined the sequence of the 152,372 bp genome of phi YS40, a lytic tailed bacteriophage of Thermus thermophilus. The genome contains 170 putative open reading frames and three tRNA genes. Functions for 25% of phi YS40 gene products were predicted on the basis of similarity to proteins of known function from diverse phages and bacteria. phi YS40 encodes a cluster of proteins involved in nucleotide salvage, such as flavin-dependent thymidylate synthase, thymidylate kinase, ribonucleotide reductase, and deoxycytidylate deaminase, and in DNA replication, such as DNA primase, helicase, type A DNA polymerase, and predicted terminal protein involved in initiation of DNA synthesis. The structural genes of phi YS40, most of which have no similarity to sequences in public databases, were identified by mass spectrometric analysis of purified virions. Various phi YS40 proteins have different phylogenetic neighbors, including myovirus, podovirus, and siphovirus gene products, bacterial genes and, in one case, a dUTPase from a eukaryotic virus. phi YS40 has apparently arisen through multiple acts of recombination between different phage genomes as well as through acquisition of bacterial genes. (c) 2006 Elsevier Ltd. All rights reserved.