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Nucleic Acids Research, 1988, Vol. 16, No. 6 2705-2715
© 1988

Articles

Evidence of natural selection to maintain a functional domain outside of the ‘core’ in a large subclass of Group I introns

Richard A. Coliins

Department of Botany, University of Toronto Toronto, Ontario, Canada

Received October 22, 1987. Revised February 15, 1988. Accepted February 15, 1988.

Comparison of three closely-related, homologous Group I introns reveals conservation of RNA secondary structure and some primary sequence outside of the characteristic Group I core structure. Further examination of forty Group I introns showed that all can be placed into one of two categories based on the length of the "loop L5" region (subtended by the base-paired sequences P and Q): short (21 to 38 bases) or long (59 to 295 bases). Despite the large variation in size and sequence, all nineteen of the long L5 introns share a common structure whose features include an adenine-rich bulge at a fixed distance from the P-Q pairing. This bulge is flanked by base-paired regions of ≥ 6 base pairs on the core-proximal side and ≥ 3 base pairs on the distal side. In the core-proximal helix there are a large number and high proportion of deviations from the consensus sequence that maintain base-pairing. These naturally-occurring compensatory base substitutions provide compelling phylogenetic support for the existence of this pairing and indicate that the conserved structure has a function in vivo.


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