
HEARO RNA motif

HNH Endonuclease-Associated RNA and ORF (HEARO) RNAs conform to a conserved RNA structure that was identified in bacteria by bioinformatics. HEARO RNAs average roughly 300 nucleotides, which is comparable to the size of many ribozymes, which catalyze chemical reactions.
Multiple lines of non-experimental evidence suggest that HEARO RNAs form part of a mobile genetic element. HEARO RNAs contain an open reading frame (ORF) that usually codes for a protein containing an HNH endonuclease domain. Members of this family of endonucleases are often used by mobile genetic elements, such as group I and group II introns, to facilitate their replication. Several instances were detected of homologous sequences where only one sequence contains the HEARO element, suggesting that the HEARO element might have integrated into an ancestor of this sequence. Such cases also suggest that HEARO elements integrate 5′ to ATGA or GTGA sequences, although no other integration requirements were elucidated. Additional analysis was consistent with the hypothesis of self replication.
The Rfam model of HEARO RNAs uses only the region that is 5′ to the ORF. This region includes the bulk of the structure, but does not include a hairpin located 3′ to the ORF.