The complete genome sequence of the Streptomyces temperate phage  C31: evolutionary relationships to other viruses

Abstract

The completed genome sequence of the temperate Streptomyces phage straight phiC31 is reported. straight phiC31 contains genes that are related by sequence similarities to several other dsDNA phages infecting many diverse bacterial hosts, including Escherichia, Arthrobacter, Mycobacterium, Rhodobacter, Staphylococcus, Bacillus, Streptococcus, Lactobacillus and Lactococcus. These observations provide further evidence that dsDNA phages from diverse bacterial hosts are related and have had access to a common genetic pool. Analysis of the late genes was particularly informative. The sequences of the head assembly proteins (portal, head protease and major capsid) were conserved between straight phiC31, coliphage HK97, staphylococcal phage straight phiPVL, two Rhodobacter capsulatus prophages and two Mycobacterium tuberculosis prophages. These phages and prophages (where non-defective) from evolutionarily diverse hosts are, therefore, likely to share a common head assembly mechanism i.e. that of HK97. The organisation of the tail genes in straight phiC31 is highly reminiscent of tail regions from other phage genomes. The unusual organisation of the putative lysis genes in straight phiC31 is discussed, and speculations are made as to the roles of some inessential early gene products. Similarities between certain phage gene products and eukaryotic dsDNA virus proteins were noted, in particular, the primase/helicases and the terminases (large subunits). Furthermore, the complete sequence clarifies the overall transcription map of the phage during lytic growth and the positions of elements involved in the maintenance of lysogeny.

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

“…for Met it is 20.2 (per thousand codons) in the host and 24.2 in the phage, for Gly it is 14.1 and 28.6, for Asn it is 24.8 and 33.8, and for Thr it is 7.2 and 17.9 (see Table 3), being consistent with the hypothesis of the translational role of phage tRNAs (Kropinski & Sibbald, 1999). Another example is seen with Streptomyces phage φC31 (Smith, Burns, Wilson, & Gregory, 1999) harboring a Thr-tRNA with the CGU anticodon, which reads the ACG codon. In the host S. coelicolor (Bentley, Chater, CerdenoTarraga, Challis, Thomson, James et al, 2002) genes, the Thr codon ACC is most heavily used (32.8 occurrences per thousand codons, see Table 3) and ACG codon is less frequently used (6.3).…”

“…Coliphage T4 harbors eight tRNA species, the anticodons of which are also shown in the table within the square brackets (Broida & Abelson, 1985). The Streptomyces phage φC31 (Smith, Burns, Wilson & Gregory, 1999) harbors a Thr-tRNA with the anticodon ACG. The genome of the Pseudomonas phage D3 encodes four tRNA genes for Met, Gly, Asn, and Thr (Kropinski & Sibbald, 1999).…”

Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are bIL170, AF009630; bIL120, AY054975; bIL15, AY054976; bIL191, AY054977; bIL77, AY054978.

“…A number of proteins reported by different authors (Gorbalenya, 1994 ;Dalgaard et al, 1997 ;Smith et al, 1999 ;Aravind et al, 2000) exhibit the same structural feature as gpl3, that is two couples of putative zinc ligands bracketing the ' HN part ' of the HNH motif, defining a potentially zinc-binding subfamily of HNH-related proteins. Some of them are part of introns (probably as homing endonucleases) whereas others are free-standing phage-or bacterial-encoded ORFs.…”

Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico

“…16). The 41 489 bp sequence of the model Streptomyces phage, φC31, has been completed only very recently (Smith et al, 1999), and has led to many interesting conclusions. For example, all of the genes are orientated in the same direction except for one which, together with its promoter and operator, appears to have been inserted from elsewhere.…”