The FMN riboswitch, also known as RFN element, is a highly conserved RNA structure that is involved in regulation of riboflavin metabolism in Bacteria. This element is a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins and regulates gene expression via either transcriptional or translational attenuation mechanisms [12456892, 12464185]. Riboflavin (vitamin B2) is an essential component of the basic metabolism, being a precursor of coenzymes flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The FMN-dependent repression of the riboflavin operon of Bacillus subtilis was shown to involve premature termination of transcription, and to be abolished by mutations in this region [18666549]. more

Sequences that could fold into a conserved RNA structure, called the RFN element, were found upstream of several genes involved in riboflavin biosynthesis in a variety of bacterial genomes, and it was suggested that regulation by the RFN element involved direct binding of FMN to mRNA [10529804]. When more bacterial genome sequences became available, comparative analysis led to the suggestion that the regulatory mechanism is based on the formation of alternative RNA structures, and that the regulation causes premature termination of transcription or inhibition of translation initiation [12136096]. Both predictions turned out to be correct. Indeed, experiments demonstrated that in B. subtilis, the rib operon is regulated at the level of transcription [12456892, 12464185], whereas the ypaA gene (aka ribU), is regulated at the level of translation [12456892]. The alignment of 61 RFN elements confirms high degree of conservation of the RFN primary and secondary structure [12136096]. The RFN element consists of five conserved helices, one variable stem-loop, and one facultative additional stem-loop (Fig. 3). The secondary structure of the RFN element predicted by the comparative analysis was confirmed experimentally by in-line probing results [12456892] and by the solved x-ray crystal structure of the FMN-bound Fusobacterium nucleatum impX RFN element [19169240]. Search for RFN elements and analysis of operon structures shows that the RFN element predomi-nantly regulates either single ribB or ribH genes, or a composite operon encoding the riboflavin biosyn-thesis genes [12136096]. In the genomic search for new RFN-regulated genes, three new types of ribo-flavin uptake transporters, namely YpaA, PnuX and ImpX, were identified [12136096]. The predicted functions of two of them, YpaA (RibU) and PnuX (RibM), were validated in the subsequent studies.