intronencoded

Intronencoded describes genetic elements in which the coding sequence is located within a self-splicing intron. The best-studied examples are intron-encoded proteins (IEPs) associated with mobile introns, especially group II introns in bacteria, archaea, and organelles, and certain group I introns that carry ORFs encoding endonucleases.

In group II introns, the intron often contains an ORF that encodes an intron-encoded protein with reverse transcriptase and maturase domains, and sometimes a DNA-binding or endonuclease domain. This IEP facilitates proper folding and splicing of the intron RNA and enables intron mobility by forming a ribonucleoprotein particle that reverse transcribes the intron and inserts it into a new genomic location.

In many group I introns, mobility is mediated by intron-encoded homing endonucleases, typically belonging to the LAGLIDADG or GIY-YIG families. These endonucleases create site-specific breaks in intronless alleles, promoting insertion and propagation of the intron through homing cycles. The intron RNA itself often participates in splicing without requiring the endonuclease for spliceosome-like catalysis.

The term intronencoded emphasizes that the functional protein or enzyme is encoded within the intron rather than elsewhere in the genome. Intron-encoded proteins illustrate the co-evolution of RNA and protein components that support intron splicing and mobility, and they are widespread in microbial genomes and organellar DNA.

Overall, intronencoded elements highlight a link between splicing RNA catalysts and protein factors that enable intron propagation and genetic diversification.