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Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review |
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| Authors: | R B Waring R W Davies |
| Institution: | University of Manchester Institute of Science and Technology, Department of Biochemistry and Applied Molecular Biology, P. O. Box 88, Manchester M U.K. |
| Abstract: | A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed. |
| Keywords: | Ribozyme mitochondria fungi protozoa Tetrahymena chloroplast splice-site alignment splice junctions An Aspergillus nidulans bp base pairs class I introns introns possessing characteristic internal conserved nueleotide sequences (Waring et al 1982) characteristic potential RNA secondary structure (Davies et al 1982) class II introns introns that like class I were first found in fungal mitochondria but which have a different characteristic potential RNA secondary structure (Michel and Dujon 1982) do not have the internal conserved sequences of class I introns COB E a non conserved sequence usually found towards the 5' end of class I introns which always pairs with the distant sequence E' to form pairing P3 E′ a non-conserved sequence that usually begins 2 bp beyond the 3' end of sequence R always pairs with sequence E IGS internal guide sequence L1 L2 L3 L4 L5 L6 regions of the proposed RNA secondary structure called “loops” because any base pairing in which bases within them may take part is not critical to the formation of the characteristic secondary structure OLI intron in gene for mitochondrial ATPase subunit 6 ORF open reading frame OX intron in gene for mitochondrial cytochrome oxidase subunit 1 P Q R S the four internal conserved nucleotide sequences typical of class I introns (Waring et al 1982) rRNA intron in gene for nuclear or mitochondrial large ribosomal RNA URF unidentified reading frame To whom all inquiries and reprint requests should be addressed at Allelix Inc 6850 Goreway Drive Mississauga Ontario L4V 1P1 Canada Tel (416) 6770831 |
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