Intron endonuclease

Kowalski, J. C., Belfort, M., Stapleton, M. A., Holpert, M., Dansereau, J. T., Pietrokovski, S., Baxter, S. M., and Derbyshire, V. (1999). Configuration of the catalytic GIYYIG domain of intron endonuclease l-Teul coincidence of computational and molecular findings. Nucleic Acids Res. 27, 2115—2125. 

Approaches to cloning DNA Genomic DNA Restriction endonucleases fragment DNA Total nuclear DNA cloned Genes contain introns cDNA Reverse transcription of mRNAs from cell Genes expressed cloned Genes have no introns... 

The fourth class of introns, found in certain tRNAs, is distinguished from the group I and II introns in that the splicing reaction requires ATP and an endonuclease. The splicing endonuclease cleaves the phosphodiester bonds at both ends of the intron, and the two exons are joined by a mechanism similar to the DNA ligase reaction (see Fig. 25-16). 

Chevalier, B.S. Stoddard, B.L. (2001) Homing endonucleases structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acid Res. 29, 3757-3774. 

Why do cells ever splice proteins It isn t clear. However, a curious fact is that many inteins are homing endonucleases.h k The genes for these nucleases are often present in introns in mRNA, and the homing endonuclease often cuts DNA in such a way as to initiate movement of its own gene (Chapter 27). The endonuclease itself is found in the center of the intein between the two end domains, which contain the catalytic centers for the splicing reaction. 

This intron must be removed in order to create a functional tRNA molecule. Its removal occurs by cleavage by an endonuclease at each end of the intron and then ligation together of the tRNA ends. This RNA splicing pathway for intron removal is totally different from that used to remove introns from pre-mRNA molecules in eukaryotes (Topic G8) and must have evolved independently. 

Intron encoded maturases. These proteins, which are normally encoded by an open reading frame (ORF) within the intron, bind specifically their own RNA and promote formation of critical tertiary contacts. In addition, most of these proteins have endonuclease and reverse-transcriptase domains, which allow intron mobility (i.e., retrotransposition and retrohom-ing) by a mechanism termed target primed reverse transcription (TPRT) (vide infra). 

A striking feature of many group II introns is that they can also attack DNA substrates (9). With assistance of intron encoded maturases or other cofactors, they can insert themselves into double-stranded DNA by TPRT. In this reaction, the intron reverse splices into one DNA strand while the endonuclease domain of the maturase cuts the second strand. The maturase then uses the cleaved target DNA as a primer for reverse transcription, which generates a DNA copy of the intron. Group II introns can catalyze more reactions than those discussed here for a more comprehensive overview on group II intron catalyzed reactions, see Reference 3. 

Nascently transcribed eukaryotic iRNAs are among the most processed of all RNA polymerase III transcripts. Like those of prokaryotic tRNAs, the 5 leader is cleaved by RNase P, the 3 trailer is removed, and CCA is added by the CCA-adding enzyme (Figure 29.25). Eukaryotic tRNAs are also heavily modified on base and ribose moieties these modifications are important for function. In contrast with prokaryotic tRNAs, many eukaryotic pre-tRNAs are also spliced by an endonuclease and a ligase to remove an intron. 

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