Microviridae, a Family Divided: Isolation, Characterization, and Genome Sequence of φMH2K, a Bacteriophage of the Obligate Intracellular Parasitic Bacterium Bdellovibrio bacteriovorus

A novel single-stranded DNA phage, MH2K, of Bdellovibrio bacteriovorus was isolated, characterized, and sequenced. This phage is a member of the Microviridae, a family typified by bacteriophage X174. Although B. bacteriovorus and Escherichia coli are both classified as proteobacteria, MH2K is only distantly related to X174. Instead, MH2K 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. Bacteriophages have been isolated and characterized from a wide range of microorganisms for more than 80 years. The vast majority of these phages are large double-stranded DNA viruses, as typified by the lambdoid, T-odd and -even families (1). Recent advances in DNA sequencing technologies and bioinformatics have facilitated the study of double-stranded DNA bacteriophage evolution (13, 14, 28). From these and other studies, a clear picture has emerged (13, 14). The prevalence of double-stranded DNA phages and prophages—cryptic, defective, and replication competent—creates an enormous pool of evolutionary material for horizontal exchange. Consequently, a mosaic spectrum of related phage species has arisen. The icosahedral, single-stranded DNA phages, or Microviridae, appear to be less common than double-stranded DNA phages. The DNAs of nine members of the family, isolated from very diverse hosts (proteobacteria, Spiroplasma, and Chlamydia), have been sequenced (11, 16, 17, 18, 22, 24–26). The species falls into two distinct subfamilies, although the subfamilies are not officially recognized in the virus taxonomy. One is represented by X174 and contains the phages that propagate in proteobacteria. The other subfamily contains phages of Chlamydia and Spiroplasma. Although these two hosts are not closely related, their phages, Chp1, Chp2, and SpV4, respectively, are quite similar. The principal difference between the two subfamilies is the existence of two genes and the complexity of major coat protein. The Chlamydia and Spiroplasma phages do not encode major spike and external scaffolding proteins. Their more-complex coat proteins contain an insertion loop that forms large threefold-related protrusions (6). Protein homologies between the two subfamilies are approximately 20% or less (6), a typical value when comparing the most distantly related members of either the lambda or T4-like groups (14, 28). However, unlike tailed doublestranded DNA families, no mosaic species that bridge the evolutionary chasms have been isolated. While the available DNA sequences suggest that the evolution of Microviridae may differ from the evolution of the moreprevalent, double-stranded DNA phages, the phages have been isolated from such distantly related hosts that only the extremes of a diversity spectrum may have been uncovered. To further elucidate the evolution of the Microviridae, we have isolated, characterized, and sequenced a new family member, MH2K, infecting Bdellovibrio bacteriovorus, a nonenterobacterial proteobacterium with an obligate intracellular parasitic life cycle similar to that of Chlamydia. The results suggest that MH2K is closely related to the phages of Chlamydia and Spiroplasma. In some instances, MH2K is more closely related to an individual chlamydiaphage than chlamydiaphages are related to each other. While the number of available Microviridae genomes is still limited, these results suggest that the forces driving single-stranded DNA phage evolution may differ from those driving double-stranded DNA phage evolution.