The ARRPOF RNA motif is a conserved RNA structure that was discovered by bioinformatics.[1]
| ARRPOF | |
|---|---|
 Consensus secondary structure and sequence conservation of ARRPOF RNA | |
| Identifiers | |
| Symbol | ARRPOF |
| Rfam | RF02933 |
| Other data | |
| RNA type | Gene; sRNA |
| SO | SO:0001263 |
| PDB structures | PDBe |
Most ARRPOF motif examples are found in environmental DNA samples, and the host organism is unknown. The only classified organism with an ARRPOF motif is Fusobacterium nucleatum, and the ARRPOF motif instance is found in the pKH9 plasmid.
It is hypothesized that the ARRPOF motif is associated with plasmid replication.[1] The pKH9 plasmid has a rep gene. Although these genes are known to be necessary for the replication of some plasmids, when this rep gene was eliminated from the pKH9 plasmid, the plasmid was still able to replicate.[2] Another region of the pKH9 plasmid was found that was necessary for replication,[2] and an ARRPOF motif occurs in part of this region.[1]
Because plasmid replication involves DNA molecules that are transiently single-stranded, it was also suggested[1] that it is possible that the ARRPOF motif functions as single-stranded DNA and not as RNA. In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available.
References
edit- ^ a b c d Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.
- ^ a b Bachrach G, Haake SK, Glick A, Hazan R, Naor R, Andersen RN, Kolenbrander PE (December 2004). "Characterization of the novel Fusobacterium nucleatum plasmid pKH9 and evidence of an addiction system". Appl. Environ. Microbiol. 70 (12): 6957–6962. doi:10.1128/AEM.70.12.6957-6962.2004. PMC 535169. PMID 15574887.