The R2 mobile element of Rhynchosciara americana: Molecular, cytological and dynamic aspects

Abstract

Ribosomal RNA genes are encoded by large units clustered (18S, 5S, and 28S) in the nucleolar organizer region in several organisms. Sometimes additional insertions are present in the coding region for the 28S rDNA. These insertions are specific non-long terminal repeat retrotransposons that have very restricted integration targets within the genome. The retrotransposon present in the genome of Rhynchosciara americana, RaR2, was isolated by the screening of a genomic library. Sequence analysis showed the presence of conserved regions, such as a reverse transcriptase domain and a zinc finger motif in the amino terminal region. The insertion site was highly conserved in R. americana and a phylogenetic analysis showed that this element belongs to the R2 clade. The chromosomal localization confirmed that the RaR2 mobile element was inserted into a specific site in the rDNA gene. The expression level of RaR2 in salivary glands during larval development was determined by quantitative RT-PCR, and the increase of relative expression in the 3P of the fourth instar larval could be related to intense gene activity characteristic of this stage. 5'-Truncated elements were identified in different DNA samples. Additionally, in three other Rhynchosciara species, the R2 element was present as a full-length element.

Processing and Translation Initiation of Non-long Terminal Repeat Retrotransposons by Hepatitis Delta Virus (HDV)-like Self-cleaving Ribozymes

“…Ribozymes were also found at 5Ј termini of many rDNA-targeting retrotransposons as follows: the R2 element in Drosophila; the termites Kalotermes flavicollis and Reticulitermes lucifugus (29), the sea squirt Ciona intestinalis (30), the black-legged tick Ixodes scapularis (GenBank accession number ABJB010506112), the horseshoe shrimp Triops cancriformis (GenBank accession number ABJB010506112), and the Zebra finch Taeniopygia guttata (20); the R4 elements (9) in the human intestinal roundworm Ascaris lumbricoides and the horse intestinal roundworm Parascaris equorum; and R6Ag1 and R6Ag3 elements (11) in A. gambiae. Partial ribozymes, missing only the 5Ј strand of P1, were found in R2 elements of the European earwig Forficula auricularia (16), the Atlantic horseshoe crab Limulus polyphemus (16,31) and the fly Rhynchosciara americana (32). In the silkworm Bombyx mori R2 element, the structure-based search uncovered the core of the HDV-like ribozyme several hundred nucleotides downstream of the retrotransposon 5Ј terminus and the putative cleavage site precisely at the 5Ј terminus of the retrotransposon, making the J1/2 region the largest found to date (Table 1).…”

Preferential Occupancy of R2 Retroelements on the B Chromosomes of the Grasshopper Eyprepocnemis plorans

“…However, the continuous reconfiguration of the rDNA locus by crossovers varies the number of R2 copies and their distribution leading eventually to R2 activity. In many insects 10–30% of the rDNA units are inserted by R2 elements, however, in other species the insertion level is lower [8], [26], [27]. Transcription of R2 elements has been found in many adult tissues of D. simulans [22] but most retrotransposition activity may take place during oogenesis and early embryo development [28].…”