Potential retroviruses in plants
Athila is a group of degenerate Arabidopsis thaliana Ty3/gypsy retrotransposons that encode a conserved ORF after integrase. The ORF may be translated on a sub-genomic RNA and has putative transmembrane domains reminiscent of a retroviral env gene. This suggests that Athila retrotransposons may produce enveloped virions and may be infectious. Athila retrotransposons are transcribed in a mutant strain of A. thaliana (ddm 1--2) that has lowered levels of DNA methylation, suggesting that they can become active. A relatively large and intact group of Athila elements was identified and is designated as the Athila4 family. Members share >90% nucleotide identity and contain only a few obvious mutations. Due to their completeness, the Athila4 family was used to reconstruct several consensus elements, which are being tested to see if they complete any of the steps in the retroelement life cycle. These experiments are required to test the hypothesis that Athila is a plant retrovirus.;Additionally, an Athila-like element from Pisum sativum, called Cyclops, was recently described, and it too has retrovirus-like features. To further characterize these elements, 18 plant species were examined for the presence of Athila-like sequences. In 14 species, elements that phylogenetically cluster with Athila were found. Five retrovirus-like element clones from Glycine max were entirely sequenced. This family is called Calypso, and it shares overall structural and sequence homology to the Athila and Cyclops retrovirus-like elements. Importantly, the env-like ORF of Calypso and Cyclops is conserved suggesting that they are evolving under functional constraints.