Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

Abstract

Hexacoral mitochondrial genomes are highly economically organized and vertebrate-like in size, structure, and gene content. A hallmark, however, is the presence of group I introns interrupting essential oxidative phosphorylation (OxPhos) genes. Two genes, encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI), are interrupted with introns. The ND5 intron, located at position 717, is obligatory in all hexacoral specimens investigated. The ND5-717 intron is a giant-sized intron that carries several canonical OxPhos genes. Different modes of splicing appear to apply for the ND5-717 intron, including conventional cis-splicing, backsplicing, and trans-splicing. Three distinct versions of hexacoral COI introns are noted at genic positions 884, 867, and 720. The COI introns are of the mobile-type, carrying homing endonuclease genes (HEGs). Some COI-884 intron HEGs are highly expressed as in-frame COI exon fusions, while the expression of COI-867 intron HEGs appear repressed. We discuss biological roles of hexacoral mitochondrial ND5 and COI introns and suggest that the ND5-717 intron has gained new regulatory functions beyond self-splicing.