The mini-ykkC RNA motif (later renamed Guanidine-II riboswitch) was discovered as a putative

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

structure that is conserved in

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

. The motif consists of two conserved

stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when ...

s whose terminal loops contain the RNA sequence ACGR, where R represents either A or G. Mini-ykkC RNAs are widespread in

Pseudomonadota Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...

, but some are predicted in other phyla of bacteria. It was expected that the RNAs are cis-regulatory elements, because they are typically located upstream of protein-coding

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s. The genes that are apparently controlled by mini-ykkC RNAs bear a resemblance to the genes controlled by

ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream of the ykkC and yxkD genes in ''Bacillus subtilis'' and related genes in other bacteria. The function of t ...

(guanidine-I), and nine gene families are common to both. Therefore, it was proposed that these two RNA classes have the same function. The complex structure and many conserved nucleotides found in the ykkC-yxkD leader are not present in the mini-ykkC RNA motif. Despite this, it was shown that each of the mini-ykkC two stem-loop structures directly binds free guanidine. Therefore, mini-ykkC RNA motif represents a distinct class of guanidine-sensing RNAs called Guanidine-II riboswitch. Its crystal structure was also determined.

References

External links

* Cis-regulatory RNA elements {{molecular-cell-biology-stub