Birth of a retroposon: the Twin SINE family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor.

SINEs are short interspersed repetitive elements found in many eukaryotic genomes and are believed to propagate by retroposition. Almost all SINEs reported to date have a composite structure made of a 5' tRNA-related region followed by a tRNA-unrelated region. Here, we describe a new type of tRNA-derived SINEs from the genome of the mosquito Culex pipiens. These elements, called TWINs, are approximately 220 bp long and reiterated at approximately 500 copies per haploid genome. TWINs have a unique structure compared with other tRNA-SINEs described so far. They consist of two tRNA(Arg)-related regions separated by a 39-bp spacer. Other tRNA-unrelated sequences include a 5-bp leader preceding the left tRNA-like unit and a short trailer located downstream of the right tRNA-like region. This 3' trailer is a 10-bp sequence that is ended by a TTTT motif and followed by a polyA tract of variable length. The right tRNA-like unit also contains a 16-bp sequence which is absent in the left one and appears to be located in the ancestral anticodon stem precisely at a position expected for a nuclear tRNA intron. According to this singular structure, we hypothesize that the TWIN: SINE family originated from an unprocessed polymerase III transcript containing two tRNA sequences. We suggest that some peculiar properties acquired by this dicistronic transcript, such as a polyA tail and a 3' stem-loop secondary structure, promote its retroposition by increasing its chances of being recognized by a reverse transcriptase encoded elsewhere in the C. pipiens genome.

CM-gag, a transposable-like element reiterated in the genome of Culex pipiens mosquitoes, contains only a gag gene.

CM-gag elements constitute an homogeneous family of sequences that are reiterated in the genome of Culex pipiens strains from different continents. Apparently complete 1.75 kb CM-gag copies are flanked by target-site duplications and have a polyadenylation signal near their 3' end. They potentially contain a unique gene encoding a putative protein that displays homologies with nucleic acid binding proteins and the gag polypeptide of retroviruses and retrotransposons, but that does not encode a reverse transcriptase. CM-gag elements are similar in their genetic organization to the telomeric transposable sequences Het-A from Drosophila melanogaster, but Southern-hybridization patterns indicate that the former are more probably dispersed in various areas of the mosquito genome. The homogeneity of CM-gag copies that are distributed worldwide suggests that they have most probably been amplified recently. Furthermore, selective constraints against amino acid changes have been acting on these sequences, suggesting that they need to encode the gag-like protein to be incorporated into the chromosomes.