Nucleotide sequence of the genome of the filamentous bacteriophage I2-2: Module evolution of the filamentous phage genome

Abstract

The nucleotide sequence of the circular single-stranded genome of the filamentous Escherichia coli phage I2-2 has been determined and compared with those of the filamentous E. coli phages Ff(M13, fl, or fd) and IKe. The I2-2 DNA sequence comprises 6744 nucleotides; 139 nucleotides less than that of the N- and I2-plasmid-specific phage IKe, and 337 (336) nucleotides more than that of the F-plasmid-specific phage Ff. Nucleotide sequence comparisons have indicated that I2-2, IKe, and Ff have a similar genetic organization, and that the genomes of I2-2 and IKe are evolutionarily more closely related than those of I2-2 and Ff. The studies have further demonstrated that the I2-2 genome is a composite replicon, composed of only two-thirds of the ancestral genome of IKe. Only a contiguous I2-2 DNA sequence of 4615 nucleotides encompassing not only the coat protein and phage assembly genes, but also the signal required for efficient phage morphogenesis, was found to be significantly homologous to sequences in the genomes of IKe and Ff. No homology was observed between the consecutive DNA sequence that contains the origins for viral and complementary strand replication and the replication genes. Although other explanations cannot be ruled out, our data strongly suggest that the ancestor filamentous phage genome of phages I2-2 and IKe has exchanged its replication module during evolution with that of another replicon, e.g., a plasmid that also replicates via the so-called rolling circle mechanism.

Imbroglios of Viral Taxonomy: Genetic Exchange and Failings of Phenetic Approaches

“…4). Examination of even this small subset of phages reveals evidence for both homologous recombination (involving genes I and IV of the phage maturation cassette [106]) and nonorthologous gene replacement (both for the replication gene cassette, noted earlier [123], and for the structural protein cassette). Thus, these phages, as with the tailed phages, cannot appropriately be described by a hierarchical taxonomy.…”

“…Yet there is ample evidence for gene exchange by both homologous recombination (99) and illegitimate means (63,123) among bacteriophages. Therefore, not only should gene exchange be considered in constructing a taxonomic framework, it effectively invalidates any taxonomy that a priori assumes that gene exchange is nonexistent.…”

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

“…Members of the Inoviridae from both genera (Inovirus and Plectrovirus) seem to enjoy frequent nonorthologous replacements within the module responsible for genome replication (Fig. 4B) (158,247,258,280). In addition, homologous recombination and intergenome rearrangements have been reported to play a role in the evolution of inoviruses (158,200,241).…”

Nucleotide sequence determination, characterization and purification of the single-stranded DNA-binding protein and major coat protein of filamentous phage Lf of Xanthomonas campestris pv. campestris

“…The nucleotide sequences of several filamentous phages of E. coli and P. aeruginosa have been determined (Beck et al, 1978;van Wezenbeek et al, 1980;Hill & Petersen, t982;Luiten et al, 1985;Peeters et al, 1985;Hill et al, 1991;Stassen et al, 1992). Comparative studies have revealed that although no DNA or amino acid sequence homology has been found, the overall gene organization is similar among these phages (Luiten et al, 1985;Stassen et al, 1992).…”

“…Comparative studies have revealed that although no DNA or amino acid sequence homology has been found, the overall gene organization is similar among these phages (Luiten et al, 1985;Stassen et al, 1992). Analysis of nucleotide sequences is the first step towards an understanding of the structure, function, organization and regulation of a 0001-1811 © 1994 SGM gene/genome.…”