Envelope-Class Retrovirus-Like Elements Are Widespread, Transcribed and Spliced, and Insertionally Polymorphic in Plants

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Abstract
Retrotransposons and retroviruses share similar intracellular life cycles and major encoded proteins, but retrotransposons lack the envelope (env) critical for infectivity. Retrotransposons are ubiquitous and abundant in plants and active retroviruses are known in animals. Although a few env-containing retroelements,gypsy-like Athila, Cyclops, andCalypso and copia-like SIRE-1, have been identified in plants, the general presence and functionality of the domain remains unclear. We show here that env-class elements are present throughout the flowering plants and are widely transcribed. Within the grasses, we show the transcription of the envdomain itself for Bagy-2 and related retrotransposons, all members of the Athila group. Furthermore, Bagy-2transcripts undergo splicing to generate a subgenomic envproduct as do those of retroviruses. Transcription and the polymorphism of their insertion sites in closely related barley cultivars suggests that at least some are propagationally active. The putative ENV polypeptides of Bagy-2 and rice Rigy-2 contain predicted leucine zipper and transmembrane domains typical of retroviral ENVs. These findings raise the prospect of active retroviral agents among the plants. [The sequence data described in this paper have been deposited as follows: Bagy-2 elements, EMBL accession nos.AF254799 and AJ279072; an alignment of 328 gypsy-likert sequences, accession no. DS44537; barley envsequences, accession nos. AJ298028–AJ298032; cDNA sequences for the spliced env subgenomic RNAs, accession nos.AJ311200–AJ311202; genomic sequences for env-classrt, accession nos. AJ295085–AJ295111; cDNA sequences forenv-class rt, accession nos. AJ295112–AJ295139; representatives of polymorphic Bagy-2 bands from IRAP gels, accession nos. AF363958, AF 363959, and AY029538.]