Introns: Splicing mysteries and evolution’s secret code

Although the participation of spliceosomes is almost always required for intron removal, a few types of genes have self-splicing RNA introns. The RNA transcript of such a gene can carry out the entire process of RNA splicing in the absence of any protein (for example, in a test tube); the intron RNA itself catalyses the process.

There are two classes of introns in which the intron RNA can function as a ribozyme to catalyse its own removal. The first class, called Group I introns, are present in the mitochondrial genome of fungi (e.g., yeast) in rRNA genes and in genes coding for components of the electron transport system; they also occur in plant mitochondrial genes, in some rRNA and tRNA genes of chloroplasts, in nuclear rRNA genes of some unicellular eukaryotes, in some tRNA genes in bacteria, and in a few bacteriophage genes coding for rnRNAs. Group I RNA introns are excised in the form of linear RNA fragments.

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In contrast, Group II introns are excised as lariats in which an adenine within the intron forms the branchpoint, just as in the spliceosome mechanism. Group II introns are found in some mitochondrial and chloroplast genes of plants and unicellular eukaryotes, and in the genomes of some archaea and bacteria. Biologists think that today’s prevailing splicing mechanism, based on spliceosomes, evolved from Group II introns, with the intron RNA’s catalytic role being taken over by the snRNA molecules of the spliceosome. Support for this idea has come from the discovery that protein-free RNA molecules isolated from spliceosomes are capable of catalysing a reaction that is closely related to the first step in the splicing reaction involving the branch-point adenine.

The burning question about introns is, why do nearly all genes in multicellular eukaryotes have them? Why do cells have so much DNA that seems to serve no coding function? Why, in generation after generation of cells, is so much energy invested in synthesising segments of DNA— and of RNA transcripts—that appear to serve no useful function and are destined only for the splicing scrap heap?

In fact, it is not true that introns never perform any functions of their own. In a few cases, intron RNAs are processed to yield functional products rather than being degraded. For example, some types of snoRNA (Small nucleolar RNAs)—whose role in guiding pre-rRNA methylation and cleavage are derived from introns that are first removed from pre-mRNA and then processed to form snoRNA. And in a few cases, introns are even translated into proteins.

But in spite of these exceptions, most introns are destroyed without serving any obvious function. One possible reason for such an apparently wasteful arrangement is that the presence of introns allows individual pre-mRNAs to be spliced in different ways, thereby generating several different mRNAs, and hence polypeptides, from the same gene. This phenomenon, called alternative RNA splicing, is made possible by the fact that individual splice sites can be either activated or skipped. As a result, a pre-mRNA molecule containing multiple introns may be spliced dozens or even hundreds of different ways. The ability to produce multiple mRNAs from a single gene may help to explain how the biological complexity of vertebrates is achieved without a major increase in the number of genes compared to simpler organisms (Humans have only about twice the number of genes as worms or flies). More than half of all human genes give rise to pre-mRNAs that are spliced in more than one way, allowing the roughly 30,000 human genes to produce mRNAs coding for more than 100,000 polypeptides.

Another interesting role proposed for introns is an evolutionary one. It is possible that introns hasten the evolution of new and potentially useful proteins. This potential role is based on the discovery that exons often code for different functional regions of polypeptide chains, each of which can independently fold into a separate domain. For example, the three exons of the β-globin gene correspond to different structural and functional regions of the polypeptide. This kind of arrangement suggests that protein-coding genes with multiple exons may have been assembled during evolution from what were originally separate entities. Introns could be involved in two ways, both of which depend on the fact that introns provide long stretches of DNA where ‘incorrect’ genetic recombination can take place without harming coding sequences. First, crossing over within introns of different genes could lead to the creation of genes containing new combinations of exons—exon shuffling. Second, recombination within other combinations of introns could easily produce duplicates of particular exons within a single gene. These exons might continue as exact duplicates, or one might mutate to a sequence that produces a new activity in the polypeptide.

Many biologists believe that introns are actually relics of ancient unicellular organisms that were the ancestors of all of today’s organisms, both prokaryotes and eukaryotes. Some support for this idea has come from the discovery that introns are present in a few of the genes of archaea and bacteria. However, over billions of years, evolutionary pressure for a streamlined genome in such unicellular organisms may have led to the loss of most of the introns that were originally present.

The author is an associate professor (retd.) and former head of the department of botany at Ananda Mohan College.