User:Jreinken/Cuckoo RNA

cuckoo RNAs are a family of small non-coding RNAs, which is conserved among several  alphaproteobacterial families. cuckoo RNAs consist of a modular RNA secondary structure with a variable number of stem-loops of similar size that carry the  conserved sequence motif CCUCCUCCC. Parts of the motif resemble an anti Shine-Dalgarno sequence and it is therefore hypothesised that cuckoo RNAs repress target mRNAs by occluding their ribosome binding site. To date, three structural variants are known that exhibit two to four stem-loops. The first cuckoo RNAs were predicted in Sinorhizobium meliloti. Subsequent studies provided experimental evidence for additional cuckoo RNAs in S. meliloti,  Rhizobium etli, Agrobacterium tumefaciens, and Rhodobacter sphaeroides. Further comparative studies especially those focusing on one of the three structural variants extended the number of known cuckoo RNAs to more than 300. While cuckoo RNAs with two stem loops are prevalent in rhodobacterial species, three and four stem-loop cuckoo RNAs are more common in the Rhizobiales.Because of this structural variation, combined with lack of sequence conservation in the helices, the family was not built with a covariance model. It was built with the alternative method of thermodynamic matchers, using the Bellman'S GAP system and software components from the RNAshapes repository.