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LOOT
Consensus secondary structure and sequence conservation of LOOT RNA
Identifiers
Symbol	LOOT
Rfam	RF03000
Other data
RNA type	Gene; sRNA
SO	SO:0001263
PDB structures	PDBe

The Latescibacteria, OD1, OP11, TM7 RNA motif (LOOT RNA motif) is a conserved RNA structure that was discovered by bioinformatics. LOOT motif RNAs are found in multiple bacterial phyla that have only recently been discovered, and are currently not well understood: Latescibacteria, OD1/Parcubacteria, OP11 AND TM7. In some cases, no specific organism has been isolated in the relevant phylum, but the existence of the bacterial phylum is known only through analysis of metagenomic sequences. Curiously, the LOOT motif is not known in any phylum that has been studied for a long time.

LOOT motif RNAs might function as cis-regulatory elements, in view of their positions upstream of protein-coding genes. Indeed, the RNAs are upstream of multiple genes that encode non-homologous proteins. If all examples of the RNA were upstream of homologous genes, there is the possibility that the RNAs were conserved in that position simply by inheritance. The non-homology of the genes downstream of LOOT RNAs makes this scenario less likely.

However, the number of different gene classes found downstream of LOOT RNAs is large in comparison to established cis-regulatory RNAs. This unusual variability in genes raises the possibility that the LOOT RNA motif has a more general function than cis regulation. A previously proposed example for the DUF805 RNA motif of a more general function is that of a Rho-independent transcription terminator, which terminates transcription (biology) of operons and is also used as a mechanism in cis-regulatory RNAs such as riboswitches. Thus a Rho-independent transcription terminator has a more general function than being an individual cis regulator. However, since some known cis-regulatory RNAs, e.g., cyclic di-GMP riboswitches do control a wide variety of genes, it is possibility that LOOT RNAs are involved in a regulatory circuit in which many gene classes can participate.

References

1. ^ Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, et al. (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Research. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.
2. Farag IF, Youssef NH, Elshahed MS (May 2017). "Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3)". Applied and Environmental Microbiology. 83 (10). Bibcode:2017ApEnM..83E.521F. doi:10.1128/AEM.00521-17. PMC 5411500. PMID 28314726.
3. Nelson WC, Stegen JC (2015). "The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle". Frontiers in Microbiology. 6: 713. doi:10.3389/fmicb.2015.00713. PMC 4508563. PMID 26257709.
4. Youssef NH, Blainey PC, Quake SR, Elshahed MS (November 2011). "Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma)". Applied and Environmental Microbiology. 77 (21): 7804–14. Bibcode:2011ApEnM..77.7804Y. doi:10.1128/AEM.06059-11. PMC 3209139. PMID 21908640.

• Non-coding RNA