Introns: Group I Structure and Function

Abstract

Group I introns fold into characteristic secondary and tertiary structures. In a Mg2+‐dependent reaction initiated by a guanosine cofactor, group I ribozymes catalyse their own excision from the primary transcript. In addition, group I introns often contain an open reading frame that assists the intron in its own mobility.

Keywords: RNA structure; self‐splicing; ribozyme; mobile genetic elements

Figure 1.

Secondary structures of group I introns. Schematic representations of the secondary structure of group I introns drawn two different ways. Dashed lines refer to exon sequences and the arrows point to the splice sites. The dot in P1 denotes the conserved GU wobble at the 5′ splice site. The universally conserved GC pair in P7 (major component of the G‐binding site) and the conserved motifs (P, Q, R and S) are shown. Note the involvement of exon sequences in both P1 and P10. The internal guide sequences (IGS) are defined as the two portions of intron sequences pairing with the exon sequences.

Figure 2.

P4–P6 domain of the Tetrahymena intron. (a) Schematic representation of the Tetrahymena intron as shown by Cate et al.. The adenosine platforms are shown underlined. Non‐Watson–Crick base pairs are indicated by dots. One of the two clamp interactions holding the helical stacks in close proximity is emphasized by a double‐headed arrow. (b) Schematic representation of the above‐mentioned clamp interaction between a GAAA tetraloop (L5b) and its receptor (J6a/6b). The stacked nucleotides of the loop and of the receptor are boxed. Tertiary contacts are shown by dotted lines. Redrawn from Cate et al.Science273: 1678–1685.

Figure 3.

Group I splicing mechanism. (a) Schematic representation of the splicing reaction of group I intron. Not shown is the need of the intron to fold into an active three‐dimensional conformation for the reaction to occur. (b) The chemistry of the first step of the splicing reaction along with proven (Mg) and putative (*) coordination sites of divalent metal ions. The chemistry of the second step is exactly the same except that the nucleophile is the 3′‐OH of the exon 1 (instead of the free guanosine) and the scissile bond is the 3′ splice site (which means that the 5′ base will be the terminal G and the 3′ portion will be the exon 2). Redrawn from Pyle (1993) Science261: 709–714.

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References

Cate JH, Gooding AR, Podell E et al. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273: 1678–1685.

Cate JH, Hanna RL and Doudna JA (1997) A magnesium ion core at the heart of a ribozyme domain. Nature Structural Biology 4: 553–558.

Chen X, Gutell RR and Lambowitz AM (2000) Functions of tyrosyl‐tRNA synthetase in splicing group I introns: an induced‐fit model for binding to the P4‐P6 domain based on analysis of mutations at the junction of P4‐P6 stacked helices. Journal of Molecular Biology 301: 265–283.

Costa M and Michel F (1995) Frequent use of the same tertiary motif by self‐folding RNAs. EMBO Journal 14: 1276–1285.

Couture S, Ellington AD, Cherry JM et al. (1990) Mutational analysis of conserved nucleotides in a self‐splicing group I intron. Journal of Molecular Biology 215: 345–358.

Golden BL, Gooding AR, Podell ER and Cech TR (1998) A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282: 259–264.

Ho Y and Waring RB (1999) The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing. Journal of Molecular Biology 292: 987–1001.

Lehnert V, Jaeger L, Michel M and Westhof E (1996) New loop‐loop tertiary interactions in self‐splicing introns of subgroup IC and ID – a complete 3D model of the Tetrahymena thermophila ribozyme. Chemistry and Biology 12: 993–1009.

Michel F and Westhof E (1990) Modeling of the three‐dimensional architecture of group I catalytic introns based on comparative sequence analysis. Journal of Molecular Biology 216: 585–610.

Piccirilli JA, McConnell TS, Zaug AJ, Noller, HF and Cech TR (1992) Aminoacyl esterase activity of the Tetrahymena ribozyme. Science 256: 805–808.

Weinstein LB, Jones BC, Cosstick R and Cech TR (1997) A second catalytic metal ion in group I ribozyme. Nature 388: 805–808.

Further Reading

Cech TR (1990) Self‐splicing of group I introns. Annual Review of Biochemistry 59: 543–568.

Doudna JA and Cate JH (1997) RNA structure: crystal clear? Current Opinion in Structural Biology 7: 310–316.

Eckstein F and Lilley DMJ (eds) (1996) Catalytic RNA. Berlin: Springer.

Edgell DR, Belfort M and Shub DA (2000) Barriers to intron promiscuity in bacteria. Journal of Bacteriology 182: 5281–5289.

Engelhardt MA, Doherty EA, Knitt DS, Doudna JA and Herschlag D (2000) The P5abc peripheral element facilitates preorganization of the Tetrahymena group I ribozyme for catalysis. Biochemistry 39: 2639–2651.

Pyle AM (1993) Ribozymes: a distinct class of metalloenzymes. Science 261: 709–714.

Saldanha R, Mohr G, Belfort B and Lambowitz AM (1993) Group I and group II introns. FASEB Journal 7: 15–24.

Silverman SK, Deras ML, Woodson SA, Scaringe SA and Cech TR (2000) Multiple folding pathways for the P4‐P6 RNA domain. Biochemistry 39: 12465–12475.

Tanner MA and Cech TR (1997) Joining the two domains of a group I ribozyme to form the catalytic core. Science 275: 847–849.

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How to Cite close
Paquin, Bruno, and Shub, David A(Apr 2001) Introns: Group I Structure and Function. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000884]