Three theories have been suggested to explain the origin of introns :4-6
A. The "introns late" theory suggests that introns and the spliceosome, the cell organelle that splices out the intron from the gene transcript to yield the mature mRNA, first originated in the eukaryotic lineages and, since then, have accumulated in the genomes of eukaryotes.2,5 Sources of new introns include "reverse splicing" and the insertion of transposable elements.5
B. The "introns early" theory proposes that the intron-exon structure of genes was present in LUCA and possibly even earlier. According to this theory, the domains ofprimordial proteins were shuffled to facilitate their diversification and evolution.3-5 Later on the introns were lost from the domains of Archaea and Bacteria. The molecular mechanism that allows intron loss is the recombination of spliced cDNA;
primitive reverse transcriptases might have mediated this loss mechanism.5 In the "intron invasion" version of"introns early", which provides a compromise between "introns early" and "introns late", it is suggested that introns appeared early but were not widespread before the emergence of eukaryotes. They became prominent only as a result of the invasion of eukaryotic genes by numerous introns at the onset of eukaryotic evolution. This invasion triggered such pivotal events in the eukaryotes as the appearance of the spliceosome, the nucleus, the linear chromosomes, the telomerase and the ubiquitin signaling system. Subsequent intron gain has been limited.7 C. The "introns first" theory, which is similar to but reaches even further back than the "introns early" theory, suggests that the introns and spliceosome are relics of the RNA world.5,6 This model is compatible with the observation that putatively ancient snoRNA genes are often specified by introns. Since RNAs were the only available catalysts for assembling an RNA protoribosome prior to the advent ofproteins, the snoRNAs would have been used for the assembly ofthe protoribosome.5,6 Therefore, according to this theory, snoRNAs predated the protein encoding exons. The processing of prerRNAs and pretRNAs by RNase P might serve as examples ofhow RNA processing might have taken place before proteins evolved.5,6 Both the "introns early" and "introns first" theories call upon known classes of enzymic reactions to handle the introns.
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