Re: Why gene structure differs in archaea, eubacteria and eukaryotes

You are correct that there are three rather equally divergent types of cellular life forms on earth: Eubacteria; Archaea; Eukaryotes. There is not any evidence that the split between these three groups was "sudden", it could have taken several hundred millions of years or even a billion years or more. The nuclear genomes of Eukaryotes (fungi, plants, animals, protists, etc) seem to be more closely related to Archaea than to Eubacteria, for example in the sequences of their DNA polymerase and ribosomal protein genes. The mitochondrial genomes, and chloroplast (in plants) genomes are more closely related to Eubacteria. It thus seems as if Eukaryotes represent Archaea that picked up intracellular Eubacteria which became obligate intracellular commensal organisms.

It is not clear whether the original cells, from which all three life forms evolved, had introns and two of the lineages have now lost the introns in order to make more compact genomes, or alternatively whether the original Eukaryotes (single-celled organisms prior to the entry of mitochondia and chloroplasts) gained introns that the original organism did not have. Some people who argue in favor of the loss of introns by Eubacteria and Archaea think that the introns would help serve as "breaks" between functional segments of proteins, so that these functional segments could be more easily "shuffled" or "recombined" to produce complex proteins made up of several small functional units.

Archaea do have some introns, which are self-splicing. The RNA itself catalyzes its own cleavage and re-joining. Eukaryotes have mostly introns which require protein plus RNA in the form of a "spliceosome" to cut and rejoin the exons, the exceptions being the mitochondrial and plastid genomes, which have self-splicing introns. The Eukaryotc intron/exon splicing process is still very poorly understood compared to many other aspects of genetics. It is not clear how alternative splicing is regulated for example. In alternative splicing, different exon combinations are spliced together to make different protein-coding messages from the same RNA transcript.