This list is not complete. Genes occasionally leap from place to place in a genome, even from one chromosome (DNA molecule) to another. This is another "rare event", but probably of great significance in evolution. There are several different mechanisms of transposition but the commonest involves the insertion of viral DNA near to the gene of interest. We mentioned this phenomenon in chapter 10; viral infection sometimes results in the viral DNA hiding in the host cell's genome. Often the virus involved in such an event is a retrovirus - it contains RNA instead of DNA - so it replicates by making a DNA copy of its RNA ("reverse transcription"). Then the DNA copy hides in the host genome. When this region of DNA is transcribed, part of the resulting RNA resembles the original retrovirus RNA; other parts include transcripts of nearby genes. The entirety of this RNA might then be reverse-transcribed and the resulting DNA inserted into a new place in the genome.
Human DNA, indeed the DNA of most organisms, contains several ghosts of ancient retroviruses, capable of jumping from place to place and carrying other genes with them. These "jumping genes" are called transposons or, more specifically, retrotransposons. Part of their role in evolution might lie in their capacity to reshuffle genes and gene control mechanisms. Another part might lie in their ability to make genes jump across species. For example, genes have been exchanged between humans and tsetse flies in Tanzania thanks to the activities of retrotransposons. It is curious to realise that retroviruses play a positive part in evolution. The most familiar example of a retrovirus is HIV, which has a bad press.
DNA is stable and well protected, but it is nowhere near as passive and static as was believed before the 1980s. In this chapter we have surveyed several recently-discovered ways in which it exhibits plasticity. These discoveries have transformed the theory of evolution.
Another unexpected feature of genes was revealed during the late twentieth century: in eukaryotes, they are not usually continuous stretches of DNA. We mentioned this in a footnote to chapter 7. The protein-coding sequences (exons) are separated by pieces of DNA (introns) that have quite different functions, or are mere "junk". During transcription, the whole length of DNA encompassing the gene is "photocopied". The transcripts of the introns have to be cut out of the RNA after transcription. Then the exon transcripts are spliced together to make the messenger. For instance, consider a gene with a promoter (P), three exons (E1, E2 and E3) and two introns (I1 and I2):-
Fig. 11.3 Intron splicing
I, and I2 transcripts cut out
Splicing messenger RNA
Fig. 11-2: removal of intron transcripts by splicing during the maturation of a messenger RNA molecule.
On the face of it, this seems a wasteful, cumbersome way of storing and expressing genetic information. Introns probably make up 80-90% of the total DNA in most eukaryotes, accounting for most of the "junk" content we alluded to earlier in this chapter. Why do introns exist? Why has evolution not eliminated them, streamlining the genome?
There are four plausible answers. First, some introns do contain useful information. For instance, they encode some small RNA molecules with exotic but essential functions in the cell. Second, an excess of non-coding DNA buffers genes against mutation, a point we mentioned earlier: the crowd protects the individual against the trigger-happy psychopath. Third, protein variants can be produced by alternative splicing. One of several alternative exons is used to make the messenger; the other alternatives are dumped. There are many examples of alternative splicing in humans. For instance, the receptors for a neurotransmitter might exist in several variant forms, but these are often encoded in a single gene. The gene transcript is alternatively spliced to give several different messenger variants. From these, the various receptor proteins are made. Thus, a single gene can encode several related proteins rather than only one.
The fourth possible advantage of the intron-exon arrangement in genes is evolutionary. Suppose one part of a gene, an exon, is transposed to a different place in the genome. (A cut through an intron does no detectable harm to the coding sequences.) The exon can then become part of another gene, generating a significantly modified protein that might have a useful new function. Evidence that such exon shuffling has actually happened in the evolutionary past is indirect, but certain domains in otherwise different proteins are remarkably similar; so it could be quite a common process and might have played a significant part in evolution.
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