Template Jumping by a LINE Reverse Transcriptase Has Created a SINE-like 5S Rrna Retropseudogene in Dictyostelium

Short interspersed nuclear elements (SINEs) are non-autonomous retroelements that mimic the 3′ ends of so-called long interspersed nuclear elements (LINEs) to ensure their propagation by proteins encoded by autonomous LINEs. The Dictyostelium discoideum genome contains a family of LINE-like retrotransposons that specifically target tRNA genes for integration (TRE elements). We describe here a retrotransposed ribosomal 5S RNA pseudogene in the D. discoideum genome that contains at its 3′ end an 8-bp sequence derived from the 3′ end of a TRE and a polyadenine tail. The r5S “retropseudogene” is flanked by target-site duplications that are characteristic for TREs, and is inserted upstream of a tRNA gene, just like a typical TRE. The D. discoideum r5S retropseudogene has structural features of a SINE, but has not been amplified, probably due to the 5′-truncation that occurred upon its initial retrotransposition. The discovery of this D. discoideum r5S retropseudogene reveals that SINEs can be created de novo during reverse transcription of LINE transcripts, if the LINE-encoded reverse transcriptase dissociates from the LINE RNA and jumps to other cellular RNAs—particularly genes transcribed by RNA polymerase III—to create continuous mixed cDNAs.