Phi29 family of phages

Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.

Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages

The genome of Bacillus subtilis bacteriophage B103 consists of double-stranded linear DNA 18,630 bp long. The DNA was sequenced, and the sequence was compared with DNA sequences of closely related phages, namely the members of the phage phi29 family. Among them, phage Nf was shown to be the most closely related to B103. Comparisons of several open reading frames (ORFs) among the family members helped to identify genes 1 and 5. A cluster of ORFs between genes 16 and 17 contains two ORFs with partial homology with two phi29 ORFs located in the same region. There are three more ORFs in this region of B103 with good ribosome binding sites (RBS) and optimal codon usage that are not homologous to any of the phi29 ORFs. The function of these five ORFs remains unexplained. It was shown that major promoters characterized in phi29 are retained in B103. Where many substitutions occur in the vicinity of a promoter, at least the -10 and -35 boxes are conserved.

Phage adsorption and productive lysis in stable protoplast type L-forms of Bacillus subtilis and Streptomyces hygroscopicus

Transferable productive lysis in stable protoplast type L-form cells of Bacillus subtilis was produced by 6 phages out of 14 strains virulent for the parent B. subtilis 170 and 1997. Most of these phages lytic for L-forms show the phi 29 morphology characteristic for the smallest B. subtilis phages containing double-stranded DNA. Among 31 actinophages, 23 of which were virulent for Streptomyces hygroscopicus, only SLE 109 and phi c 31 gave productive infection of the stable protoplast type L-form of S. hygroscopicus NG 33--354. Electron microscopic investigation and treatment by DNAse demonstrated that infection of L-form cells is an adsorption-injection process, and that it is not caused by transfection of free phage DNA or endocytotic uptake of phage particles. Because in both stable L-forms cell wall biosynthesis is blocked irreversibly the results allow the conclusion that specific receptors must be localized in the cytoplasmic membrane for those phages producing transferable lysis in protoplast type L-forms. Localization of receptors for certain phages in the cytoplasmic membrane seems to occur in many Gram-positive bacteria, but not in Gram-negative bacteria.