Genome Comparison and Proteomic Characterization of Thermus thermophilus Bacteriophages P23-45 and P74-26: Siphoviruses with Triplex-forming Sequences and the Longest Known Tails

Abstract

The genomes of two closely related lytic Thermus thermophilus siphoviruses with exceptionally long (~800 nm) tails, bacteriophages P23-45 and P74-26, were completely sequenced. The P23-45 genome consists of 84,201 bp with 117 putative ORFs (Open Reading Frames), and the P74-26 genome has 83,319 bp and 116 putative ORFs. The two genomes are 92% identical with 113 ORFs shared. Only 25% of phage gene product functions can be predicted from similarities to proteins and protein domains with known functions. The structural genes of P23-45, most of which have no similarity to sequences from public databases, were identified by mass-spectrometric analysis of virions. An unusual feature of the P23-45 and P74-26 genomes is the presence, in their largest intergenic regions, of long polypurine-polypyrimidine (R-Y) sequences with mirror repeat symmetry. Such sequences, abundant in eukaryotic genomes but rare in prokaryotes, are known to form stable triple helices that block replication and transcription and induce genetic instability. Comparative analysis of the two phage genomes shows that the area around the triplex-forming elements is enriched in mutational Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access

Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae

“…3). For example, homologues of the genes with predicted function in host recognition and cell entry (ORF28-ORF31 in P23-77 and ORF22-ORF26 in IN93) are found in the genomes of unrelated tailed siphoviruses P23-45 and P74-26, which also infect T. thermophilus [38]. Similarly, IN93 ORF24 and ORF43 despite having no relatives within P23-77 and related proviruses are also present in the same two siphoviruses.…”

The putative small terminase from the thermophilic dsDNA bacteriophage G20C is a nine-subunit oligomer

“…However, as the small terminase is usually encoded by a gene immediately preceding the large terminase and portal protein genes, and because the corresponding G20C gene had an appropriate size, we decided to clone this gene of G20C. This gene corresponds to the ORF P23p84 (UniProtKB/TrEMBL A7XXB6) in the closely related phage P23-45 (Minakhin et al, 2008). Forward and reverse primers containing the NdeI and HindIII restriction-site sequences, respectively, enclosing the full-length protein were designed as follows: forward, 5 0 -GGA-CAACATATGAGCGTGAGTTTTAGGGAC-3 0 ; reverse, 5 0 -GGCA-AGCTTCTAGGTCTTAGGCGCTTCATC-3 0 .…”

“…To answer some of these questions, we initiated structural and functional studies on the putative small terminase protein from the Thermus thermophilus bacteriophage G20C, which is a close relative of bacteriophages P23-45 and P74-26 (Minakhin et al, 2008). Here, we report the production of recombinant protein in Escherichia coli, protein purification and crystallization.…”

The Closest Relatives of Icosahedral Viruses of Thermophilic Bacteria Are among Viruses and Plasmids of the Halophilic Archaea

“…ABU97052, BLAST E-value 2.2eϪ12) and P23-45 (GenBank no. ABU96936, E-value 8.1eϪ12), both assigned to the Siphoviridae family (54). A wide distribution of a potential capsid associated lysozyme among nonhomologous Thermus phages suggests that the activity of VP29-like proteins is crucial for the survival of Thermus viruses.…”