|Introns with coding sequences
In fungal mitochondria, for some genes, it was shown that introns may code for RNA
maturases or endonucleases which take part in RNA processing, and DNA recombination respectively (see Expression of Gene : Protein Synthesis 3. RNA Processing (RNA Splicing, RNA Editing and Ribozymes)
for more details).
Two hypotheses for origin of mRNA introns - 'early intron' and 'late intron'
Although introns are generally absent in protein-coding genes of bacteria, archaebacteria and some lower eukaryotes, class II type of self splicing introns have recently been reported even in bacteria. Such a distribution of introns has been used for a study of the role of introns in the evolution of genes or alternatively for a study of the origin of introns themselves. There are two different hypotheses available in this connection, (i) According to 'early- intron hypothesis,
(also called "exon theory of genes" by Walter Gebert, 1987), ancestral exons existed as independent genetic units or microgenes and their association with introns helped generation of diversity in genes through trans-splicing and exon shuffling.
There are examples, where new genes could be generated by exon shuffling through intron recombination events. This and several other known events are used as evidences in favour of early intron hypothesis, (ii) According to 'late -intron hypothesis' (also called the "insertional theory of intron origins"), intron evolution was independent of the evolution of protein-coding genes. It is assumed in this hypothesis, that the self-splicing introns invaded the genome of eukaryotic ancestor, as endosymbionts and evolved into mitochondria and chloroplasts containing class II introns. It is postulated that invasion took place at the mRNA level, which was followed by reverse transcription and recombination with DNA, producing split genes. These introns gave other types of introns later. This explains, why introns are absent in bacteria, archaebacteria and lower eukaryotes. The recent report of introns in bacteria may be the initial stage of this process, of the evolution of introns.
Efforts are being made to combine the two above hypotheses using strong features of both to formulate a new intermediate hypothesis.