1. Introduction

23.8 Summary

Self-splicing is a property of group I introns, found in Tetrahymena and Physarum nuclei, in fungal mitochondria, and in phage T4. The information necessary for the reaction resides in the intron sequence (although the reaction is actually assisted by proteins in vivo). The reaction requires formation of a specific secondary (and presumably tertiary) structure involving short consensus sequences. The RNA creates a structure in which the substrate sequence is held by the IGS region of the intron, and other conserved sequences generate a guanine nucleotide binding site. It occurs by a transesterification involving a guanosine residue as cofactor. No input of energy is required. The guanosine breaks the bond at the 5′ exon-intron junction and becomes linked to the intron; the hydroxyl at the free end of the exon then attacks the 3′ exon-intron junction. The intron cyclizes and loses the guanosine and the terminal 15 bases. A series of related reactions can be catalyzed via attacks by the terminal G-OH residue of the intron on internal phosphodiester bonds. By providing appropriate substrates, it has been possible to engineer ribozymes that perform a variety of catalytic reactions, including nucleotidyl transferase activities.

Some group I and some group II mitochondrial introns have open reading frames. The proteins coded by some group I introns are endonucleases that make double-stranded cleavages in target sites in DNA; the cleavage initiates a gene conversion process in which the sequence of the intron itself is copied into the target site. Group II introns code reverse transcriptase activities that enable an RNA copy of the intron to be copied into the target site. These types of introns probably originated by insertion events.

Catalytic reactions are undertaken by the RNA component of the RNAase P ribonucleoprotein. Virusoid RNAs can undertake self-cleavage at a "hammerhead" structure. Hammerhead structures can form between a substrate RNA and a ribozyme RNA, allowing cleavage to be directed at highly specific sequences. These reactions support the view that RNA can form specific active sites that have catalytic activity.

RNA editing changes the sequence of an RNA after or during its transcription. The changes are required to create a meaningful coding sequence. Substitutions of individual bases occur in mammalian systems; they take the form of deaminations in which C is converted to U, or A is converted to I. A catalytic subunit related to cytidine or adenosine deaminase functions as part of a larger complex that has specificity for a particular target sequence.

Additions and deletions (most usually of uridine) occur in trypanosome mitochondria and in paramyxoviruses. Extensive editing reactions occur in trypanosomes in which as many as half of the bases in an mRNA are derived from editing. The editing reaction uses a template consisting of a guide RNA that is complementary to the mRNA sequence. The reaction is catalyzed by an enzyme complex that includes an endonuclease, terminal uridyltransferase, and RNA ligase, using free nucleotides as the source for additions or releasing cleaved nucleotides following deletion.