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Intron

Intron

Certain introns act as ribozymes and splice themselves out.

Different Classes of Intron Show Different Splicing Mechanisms

There are several classes of introns (Table 12.01). The GT-AG (or GU-AG in RNA code) introns described above are by far the most frequent in eukaryotic nuclear genes. The AT-AC (or AU-AC) introns are extremely similar to the GT-AG introns except for their different intron boundary sequences. They are processed in an almost identical manner, by a different, but closely related, set of splicing factors.

Group I introns are self-splicing. The RNA itself provides the catalytic activity and thus acts as an RNA enzyme or ribozyme. No proteins are required for splicing. The folding of the RNA into a series of base-paired stem and loop structures is needed for ribozyme activity. The 3-dimensional structure is folded so as to bring the two splice sites together and to strain the bonds that will be broken. The reaction pathway starts with the guanosine of any of GMP, GDP or GTP attacking the 5' splice site (Fig. 12.12) and cutting the exon and intron apart. Note that the guanosine nucleotide is free in solution and is not part of the RNA. The free exon-3'-OH then reacts with the downstream splice site. Group I introns include those in the rRNA of lower eukaryotes, such as the single-celled, ciliated freshwater protozoan, Tetrahymena. However, most are found in genes of mitochondria and chloroplasts. Occasional cases occur in bacteria and bacteriophages.

Exon 1

Exon 2

Exon 1

Exon 1

Exon 2

self-splicing Splicing out of an intron by the ribozyme activity of the RNA molecule itself without the requirement for a separate protein enzyme

A) Group i self-splicing B) Group ii self-splicing

FIGURE 12.12 Group I and Group II Intron Self-Splicing Reactions

In both Group I and Group II self-splicing introns, the intron folds up so as to bring the ends of the two exons together (not shown). For clarity, here we have indicated only the first level of intron folding by base pairing. A) In Group I introns, the 5' splice site is attacked by a soluble guanosine nucleotide which cuts the exon and intron apart. Next, the free 3' OH group of the exon reacts with the 3' splice site and promotes the joining of the two exons (which are actually held close together). B) The self-splicing reaction in Group II introns is similar to Group I, except that an internal adenosine initiates splicing.

FIGURE 12.12 Group I and Group II Intron Self-Splicing Reactions

In both Group I and Group II self-splicing introns, the intron folds up so as to bring the ends of the two exons together (not shown). For clarity, here we have indicated only the first level of intron folding by base pairing. A) In Group I introns, the 5' splice site is attacked by a soluble guanosine nucleotide which cuts the exon and intron apart. Next, the free 3' OH group of the exon reacts with the 3' splice site and promotes the joining of the two exons (which are actually held close together). B) The self-splicing reaction in Group II introns is similar to Group I, except that an internal adenosine initiates splicing.

Group II introns are found in the organelles of fungi and plants and occasional examples occur in prokaryotes. Group III introns are found in organelles. Both classes are also self-splicing. However, the reaction is started by attack of an internal adeno-sine (not a free nucleotide as in Group I introns) (Fig. 12.12). This results in a lariat structure being formed, as in the typical nuclear pre-mRNA introns described above. These three types of intron may thus have a common evolutionary origin. Group III introns are similar to Group II introns, but are smaller and have a somewhat different 3-dimensional structure.

Twintrons are complex arrangements in which one intron is embedded within another. They consist of two or more Group I, Group II or Group III introns. Since introns are embedded within other introns, they must be spliced out in the correct order, innermost first, rather like dealing with parentheses in algebra.

Archeal introns are found in tRNA and rRNA and are similar in some respects to eukaryotic pre-tRNA introns. No complex splicing occurs; no snurps are needed and no ribozymes are involved. The tRNA and rRNA precursors fold up into their normal 3D structures with the intron forming a loop. This loop can be cut out by a ribonuclease and the ends joined by an RNA ligase. Their stable 3-dimensional structures hold the two halves of the tRNA and rRNA molecules together during cleavage and ligation and there is no need for extra factors such as snRNPs for recognition or processing.

Alternative Splicing Produces Multiple Forms of RNA

Although any particular splice junction must be made with total precision, eukaryotic cells can sometimes choose to use different splice sites within the same gene. Generally, alternative splicing is used by different cell types within the same animal. This alternative splicing Alternative ways to make two or more different final mRNA molecules by using different segments from the same original gene

Introns are found in Archaea but are removed by simple ribonucleases without needing a splicesome.

Promoter #1

Promoter #2

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