Plant Endogenous Retroviruses? A Case of Mysterious ORFs

Endogenous retroviruses have traditionally been defined as descendants of extinct retroviruses that infected and integrated into the chromosomes of host germ-line cells and were thereafter transmitted vertically as part of host genomes. Most retain at least the vestiges of genes once required for infectious horizontal transfer, namely envelope genes. In contrast, the long evolutionary histories of retrotransposons are presumed not to have included infectious ancestors. With the characterization of the Gypsy retrotransposon in Drosophila melanogaster as an infectious, endogenous retrovirus, these distinctions have blurred. A number of plant LTR retroelements possess coding regions whose conceptual translations produce hypothetical proteins with predicted structural elements found in viral envelope proteins, and the term endogenous retrovirus began to be applied to these elements. The question of whether any of the many plant retroelement genes now annotated as “env-like” generate proteins that have or had envelope functions remains unanswered. This review reevaluates the available data.