Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus

Abstract

A novel single-stranded DNA phage, phiMH2K, of Bdellovibrio bacteriovorus was isolated, characterized, and sequenced. This phage is a member of the Microviridae, a family typified by bacteriophage phiX174. Although B. bacteriovorus and Escherichia coli are both classified as proteobacteria, phiMH2K is only distantly related to phiX174. Instead, phiMH2K exhibits an extremely close relationship to the Microviridae of Chlamydia in both genome organization and encoded proteins. Unlike the double-stranded DNA bacteriophages, for which a wide spectrum of diversity has been observed, the single-stranded icosahedral bacteriophages appear to fall into two distinct subfamilies. These observations suggest that the mechanisms driving single-stranded DNA bacteriophage evolution are inherently different from those driving the evolution of the double-stranded bacteriophages.

FIG. 1.

Genetic maps of φMH2K, Chp2 (18), and φX174 (25). Reading frames that encode proteins with Chp2 homologues were designated with the same numbers used in the Chp2 genetic map (18). Reading frames that are not found in Chp2 were assigned letters. The numbering of the nucleotides commences with the start codon of gene 1.

FIG. 2.

Electron micrograph of φMH2K. Magnification, ×31,500. Bar, 100 nm.

FIG. 3.

Multiple-sequence alignment of coat proteins of Microviridae phages. Different colors were added to give a better representation of the similarities between the eight sequences. The four φX174-like phages are grouped on the bottom; the smaller Microviridae are grouped at the top. Amino acids identical in all sequences (red boldface type) and conserved (green boldface type) and semiconserved (blue boldface type) substitutions in all sequences are indicated. Amino acids identical within the subgroups (red type) and conserved (green type) and semiconserved (blue type) substitutions within the subgroups are indicated. Dashes represent gaps introduced to maximize alignment of the sequences. The secondary structure (2°) of φX174 is presented on the last line. The yellow arrows represent β-strands, and the green cylinders represent α-helices.