REPINs are facultative genomic symbionts of bacterial genomes

Relationships among organisms, in which one lives inside of another, with benefits accruing to both partners, are referred to as endosymbiotic. Such relationships are common in the biological world, yet descriptions are confined to organismal life. Here we argue that short sequence repeats known as REPINs - whose replication is dependent on a non-jumping RAYT transposase - form a similar facultative symbiotic relationship with the bacterial chromosome. Evidence stems from distribution patterns across the eubacteria: persistence times of many millions of years, exceedingly rare duplication rates, vertical transmission, and population biology typical of living organisms, including population size fluctuations that correlate with available genome space. Additional analysis of patterns of REPIN evolution conform with theoretical predictions of conflict (and resolution) arising from the effects of selection operating simultaneously on REPINs and host cells. A search for similar kinds of genomic symbionts suggests that the REPIN-RAYT system is not unique.