Title: The Cyanobacterial dnaX Intein Encodes an Out-of-Frame Homing Endonuclease and is Sporadically Distributed in the Phylum

Inteins are self-splicing proteins with a wide distribution in single-celled organisms, viruses, and plastids. The function of inteins remains an unanswered question. They may be regulatory elements as they must splice out of their host protein. However, recent research findings point to inteins likely being mobile selfish genetic elements capable of horizontal transfer. Here the intein inhabiting cyanobacterial DNA Polymerase III gamma/tau subunit (dnaX) serves as a case study into the conservation and phylogenetics of the intein compared to the host extein. Phylogenetic analysis reveals a sporadic distribution of intein alleles having an evolutionary history that is incongruent with the extein that may reticulate independently across clades. The dnaX intein can also contain an out-of-frame homing endonuclease (HE), a rarity for annotated inteins, that may have been the result of secondary invasion of an HE into a mini-intein. The simultaneous presence of intein-free and intein-containing alleles in populations of Microcystis aeruginosa challenges current theories about the life cycles of homing endonuclease containing selfish genetic elements and suggests that alternatives to the homing cycle need to be considered for intein persistence. Our analysis reveals an incongruent, disjointed distribution of this specific intein, suggesting that it is neither conserved among individual cyanobacterial lineages nor a critical component of dnaX functionality yet is able to persist in populations without being lost.