Population Dynamics of Archaeal Mobile Introns in Natural Environments: A Shrewd Invasion Strategy of the Latent Parasitic DNA

Abstract

A body of data has been amassed in recent years, which shows the existence of introns within rRNA gene loci of certain archaeal lineages. Most striking is that the introns are optional, present in some strains and absent in others. They often have a nested gene encoding a LAGLIDADG-type site-specific DNA endonuclease known as "homing endonuclease (HE)". Such introns are, therefore, assumed to be "mobile introns", which propagate horizontally by using the "homing" pathway.
The phenomenon whereby mobile introns are inserted into the archaeal rRNA gene loci and disperse within a population to create genome polymorphism can be interpreted as "selfish behavior" of HE genes. The intron-encoded HE does not break rRNA genes containing the introns, but acts selectively to break only the intronless alleles. In other words, HE destroys alleles which do not possess internally a copy of its own gene by introducing a double strand DNA break (DSB), thus endangering the continued existence of the host's genome in that failure to repair the DSB will prove lethal. Moreover, in making its own gene into a mould for the purpose of recombination, it is adopting the horizontal propagation strategy to increase the copy number of its own gene within the population.
HE is a vital factor in the propagation of this type of mobile intron, and it is a noteworthy fact that the HE gene is "neutral", being neither advantageous nor disadvantageous to the existence of the host. Since the HE gene is removed along with the intron in the splicing process, it has no effect on the functional expression of the rRNA gene. Here, we discuss the dynamics whereby these molecular parasites, which reside in the archaeal genomes, propagate and evolve within a population.