MsiK RNA motif

msiK RNA motif
Consensus secondary structure of msiK RNAs
Identifiers
Symbol	msiK RNA
Rfam	RF01747
Other data
RNA type	Cis-regulatory element
Domain(s)	Actinobacteria

The msiK RNA motif describes a conserved RNA structure discovered using bioinformatics.^[1] The RNA is always found in the presumed 5' untranslated regions of genes annotated as msiK, and is therefore hypothesized to be an RNA-based cis-regulatory element that regulates these genes.

MsiK, the protein encoded by msiK genes, is the ATPase subunit within certain ABC-type membrane transporter proteins. MsiK is thought to allow the import of multiple kinds of complex sugars.^[2] Based on analysis of various experimental reports, it was suggested that msiK RNAs are probably not involved in sensing glucose themselves, but are more likely a part of a feedback inhibition process to regulate levels of the MsiK protein.^[1]

The msi RNA motif is a hairpin with a conserved 11-nucleotide bulge (see secondary structure), as shown in the diagram. A Shine-Dalgarno sequence (predicted ribosome-binding site) overlaps a part of the msiK RNA. If msiK RNAs are cis-regulatory elements, they likely function by sequestering the ribosome-binding site, thus preventing gene translation.

References

1. ^ ^{a b} Weinberg Z, Wang JX, Bogue J, et al. (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2864571. 
2. ^ Bertram R, Schlicht M, Mahr K, Nothaft H, Saier MH, Titgemeyer F (March 2004). "In silico and transcriptional analysis of carbohydrate uptake systems of Streptomyces coelicolor A3(2)". J. Bacteriol. 186 (5): 1362–73. PMC 344420. PMID 14973030. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=344420. 

External links

• Rfam page for msiK RNA