STRUCTURAL CONSTRAINTS IN EXPANSION SEGMENTS FROM A MIDGE 26S RDNA

DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once al igned with their Drosophila counterparts, sequence and base content co mparisons were carried out. Sequence identity was found to be high ove rall, except for six regions that displayed a local bias in nucleotide composition toward AT. These regions were identified as expansion seg ments D3, D4, D5, D6, D7a, and D12. Besides base sequence divergence, differences in length were observed between the respective variable do mains of the two species, particularly for D7a. Prediction of secondar y structure showed that the folding of the Chironomus expansion segmen ts analyzed is in agreement with the general patterns proposed for euk aryotic LSU rRNA. The comparison with Drosophila revealed also that th e Chironomus secondary structures of the variable domains are supporte d by multiple compensatory substitutions or even compensatory insertio ns. Chironomus D7a displayed an unusual structural feature with respec t to the insect D7a models that have been inferred up to now. The stru ctural constraint observed in the expansion segments of Diptera so dis tantly related as midges and Drosophila suggests that these regions co ntribute to some functional role. Concerning the D7a of insects so far analyzed, there can be, in addition to a conserved secondary structur e, a nucleotide composition constraint that might be important for the process giving rise to the alpha and beta halves of the 26S rRNA.