Characterization of φ12, a Bacteriophage Related to φ6: Nucleotide Sequence of the Large Double-Stranded RNA

Abstract

The isolation of additional bacteriophages besides phi6 containing segmented double-stranded RNA genomes (dsRNA) has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the large double-stranded RNA genomic segment of bacteriophage phi12 was copied as cDNA and its nucleotide sequence determined. This genome's organization is similar to that of the large segment of bacteriophages phi6, phi8, and phi13. In the amino acid sequence of the viral RNA-dependent RNA polymerase (P2), similarity was found to the comparable proteins of phi6, phi8, and phi13. Amino acid sequence similarity was also noted in the nucleotide triphosphate phosphorylase (P4) to the comparable proteins of phi8 and phi13.

New enveloped dsRNA phage from freshwater habitat

“…The genetic organization of wNN resembles that of w6 and other identified cystoviruses (Gottlieb et al, , 2002Hoogstraten et al, 2000;McGraw et al, 1986;Mindich et al, 1988;Qiao et al, 2000Qiao et al, , 2010, and putative functions could be assigned to the ORFs based on chromosomal position, size and sequence homology with w6 ( Fig. 2, Table 1).…”

“…Similarly, the ribosome-binding sites of ORFs 6 and 13 were non-optimal. Polar relationships between genes have also been demonstrated for other cystoviruses (Gottlieb et al, 2002;Hoogstraten et al, 2000;McGraw et al, 1986;Mindich et al, 1988;Qiao et al, 2000Qiao et al, , 2010.…”

“…All in all, the genetic organization is relatively conserved within the identified cystoviruses, and the ORFs/genes cluster into functional groups (Gottlieb et al, , 2002Hoogstraten et al, 2000;McGraw et al, 1986;Mindich et al, 1988;Qiao et al, 2000Qiao et al, , 2010. For instance, the highly conserved Lsegment includes ORFs/genes encoding the components of the virion core containing the polymerase activity (Figs 1d and 2) whereas the M-segment, which varies the most among cystoviruses, contains ORFs/genes encoding envelope proteins (Figs 1d and 2).…”

“…Similarly to other cystoviruses, all the ORFs of the wNN genome are oriented in the same direction (Gottlieb et al, , 2002Hoogstraten et al, 2000;McGraw et al, 1986;Mindich et al, 1988;Qiao et al, 2000Qiao et al, , 2010. The ORFs contain a translational initiation codon AUG, except for ORFs 5 and 10, which begin with the codon GUG.…”

“…All isolates were obtained from plant debris in the USA, and they infect Gram-negative bacteria, mainly phytopathogenic Pseudomonas syringae strains. Complete genome sequences are available for four cystoviral isolates in addition to w6 (Gottlieb et al, , 2002Hoogstraten et al, 2000;McGraw et al, 1986;Mindich et al, 1988;Qiao et al, 2000Qiao et al, , 2010. Some cystoviruses are genetically remarkably similar to w6, whereas others are only distantly related.…”