Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants

Abstract

Although integration of viral DNA into host chromosomes occurs regularly in bacteria and animals, there are few reported cases in plants, and these involve insertion at only one or a few sites. Here, we report that pararetrovirus-like sequences have integrated repeatedly into tobacco chromosomes, attaining a copy number of Ϸ10 3 . Insertion apparently occurred by illegitimate recombination. From the sequences of 22 independent insertions recovered from a healthy plant, an 8-kilobase genome encoding a previously uncharacterized pararetrovirus that does not contain an integrase function could be assembled. Preferred boundaries of the viral inserts may correspond to recombinogenic gaps in open circular viral DNA. An unusual feature of the integrated viral sequences is a variable tandem repeat cluster, which might reflect defective genomes that preferentially recombine into plant DNA. The recurrent invasion of pararetroviral DNA into tobacco chromosomes demonstrates that viral sequences can contribute significantly to plant genome evolution. M ost plant viruses have single-stranded RNA genomes. Only two classes of plant viruses, caulimoviruses and badnaviruses, contain genomes of double-stranded DNA (1). Because these double-stranded DNA viruses use a virally encoded reverse transcriptase to replicate their genomes, they, together with vertebrate hepadnaviruses, are classified as pararetroviruses to distinguish them from true retroviruses, which have RNA genomes. Retroviruses have not yet been conclusively identified in plants, although recent findings of retrotransposons that encode envelope-like proteins suggest that they might exist (2-4). Pararetrovirus replication in plants proceeds by nuclear transcription of a slightly greater than genome-length RNA with terminal repeats that is generated by the host RNA polymerase II. This is followed by reverse transcription in the cytoplasm of the terminally redundant RNA, which also serves as an mRNA for viral proteins (5). Although retrovirus DNA integrates into host chromosomes by means of a virally encoded integrase (6), pararetroviruses generally lack the gene for this enzyme, and integration is not required for virus replication. However, pararetroviral DNA can in principle integrate into host DNA, as exemplified by mammalian hepatitis B (hepadna)virus, which has been found integrated into host chromosomes in hepatic tissue, where it is associated with liver carcinomas (7). Until recently, there were no data suggesting comparable integration of pararetroviral sequences into plant DNA.In contrast to bacterial and animal viruses, plant viral sequences are generally thought to integrate rarely, if at all, into host genomes. One well characterized example concerns a single insertion of sequences related to a geminivirus, which has a single-stranded circular DNA genome, into tobacco nuclear DNA (8-10). Although the geminivirus case has been considered exceptional, several recent reports prompt a reconsideration of the possibility that plant pararetrovirus DNA might integr...

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