ELSEVIER Biochimica et Biophysica Acta 1217 (1994) 147-155 BB Biochi~ic~a et Biophysica A~ta Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure K.M. Kjer *, G.D. Baldridge, A.M. Fallon University of Minnesota, Department of Entomology, 1980Folwell Avenue, St. Paul, MN 55108, USA (Received 3 May 1993;revised manuscript received21 July 1993) Abstract We report the sequence and propose a secondary structure for the cytoplasmic large subunit (5.8S and 28S) ribosomal RNA of the mosquito, Aedes albopictus, in an aligned format that incorporates secondary structure comparisons with Homo sapiens, Drosophila melanogaster, and Escherichia coli ribosomal RNAs. This format facilitates comparison of subtle differences between models, allowing nucleotide by nucleotide analysis at each position of discrepancy. Comparison of the A. albopictus large subunit ribosomal RNA gene with those from other species revealed new compensatory base changes. The aligned format focuses attention to the specific contribution of the A. albopictus sequence by facilitating comparison with the sequence of another dipteran, D. melanogaster. This is the second report of a complete large subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a member of the lower Diptera (Nematocera). Key words: ribosomal RNA; RNA structure; rRNA sequence; Secondary structure; Ribosome; (Mosquito) 1. Introduction Refinement of ribosomal RNA (rRNA) secondary structure is critical to interpretation of RNA-protein and RNA-RNA interactions within the ribosome and underlies development of a meaningful tertiary struc- ture of the ribosome. Proposed base pairing regions in rRNA molecules are typically validated by compen- satory base changes (CBCs), which allow sequence divergence but preserve rRNA secondary structure among diverse organisms. A comparative approach to structural modeling of the large subunit rRNA was initially used to develop the secondary structure of prokaryotic 23S rRNA [1-3] and has been extended to the large subunit rRNAs from a variety of eukaryotic species [4-10]. Structural proposals for small subunit rRNAs have also been compiled [11-13]. Typically, the rationale behind proposed interactions is not provided in models of secondary structure, probably due to the * Corresponding author. Present address: Brigham Young Univer- sity, Department of Zoology,Provo, UT 84602, USA. 0167-4781/94/$07.00 © 1994 Elsevier Science B.V. All rights reserved SSDI 0167-4781(93)E0227-F difficulty in incorporating CBC evidence in two-dimen- sional formats. In this paper, we report the sequence and secondary structure of A. albopictus large subunit rRNA. We present both sequence and structure in an aligned format that includes the comparison of three differing and recent structural proposals, and permits the de- scription of comparative evidence. Although we began the present study without assumptions about the valid- ity of one proposal over another, comparative analysis suggested that the most recent Escherichia coli struc- ture [14] was more compatible with predicted A. al- bopictus secondary structures than any of the eukary- otic proposals made before 1990. 2. Materials and methods Sequencing For sequence analysis, restriction fragments from A. albopictus large subunit rRNA genes in EMBL 3 bacteriophage clones E3 and E5 [15] were subcloned in Bluescript II vectors (Stratagene, La Jolla, CA). The 28S rRNA gene from clone E5 was sequenced in its