Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages

Abstract

The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two genera: the alloleviviruses, like Qβ, which have a coat read-through protein, and the leviviruses, like MS2, which do not have this coat protein extension. AP205 has no read-through protein and may therefore be classified as a levivirus. A major digression from the known leviviruses is the apparent absence of a lysis gene in AP205 at the usual position, overlapping the coat and replicase proteins. Instead, two small ORFs are present at the 5′ terminus, preceding the maturation gene. One of these might encode a lysis protein. The other is of unknown function. Other new features concern the 3′-terminal sequence. In all ssRNA coliphages, there are always three cytosine residues at the 3′ end, but in AP205, there is only a single terminal cytosine. Distantly related viruses, like AP205 and the coliphages, do not have significant sequence identity; yet, important secondary structural features of the RNA are conserved. This is shown here for the 3′ UTR and the replicase-operator hairpin. Interestingly, although AP205 has the genetic map of a levivirus, its 3′ UTR has the length and RNA secondary structure of an allolevivirus. Sharing features with both MS2 and Qβ suggests that, in an evolutionary sense, AP205 should be placed between Qβ and MS2. A phylogenetic tree for the ssRNA phages is presented.