Collection of regulogs for Lysine (RF00168) RNA regulatory element
The Lysine riboswitch, also known as LYS element and L box riboswitch, is a highly conserved RNA structure that is involved in regulation of lysine metabolism in Bacteria. It serves as a riboswitch that binds directly to the amino acid lysine to regulate gene expression via either transcriptional or translational attenuation mechanisms [14597663, 14523230].
Initially, a regulatory mechanism involving an upstream terminator for lysC in Bacillus subtilis has been demonstrated . A lysine riboswitch (L-box or LYS element) was initially suggested  and then studied using comparative genomics [14627808, 14523230] and in structural mapping experiments .
It was shown that in B. subtilis lysine binds to the L-box structure upstream of lysC . This causes a transition to the structure with a terminator, and the subsequent premature termination of transcription.
The alignment of 71 LYS elements confirms high degree of conservation of the LYS primary and secondary structure . The LYS element consists of seven conserved helices, and single-stranded regions (Fig. 4). The solved x-ray crystal structure of the lysine riboswitch showed that the lysine amino acid is bound in the pocket formed by three helical bundle and a two helical bundle joined by the 5-way junction . Genetic experiments with RNA motif of the lysC gene in B. subtilis provided insight into the molecular mechanisms employed by L box riboswitch RNAs to bind and recognize lysine .
Search for LYS elements and analysis of operon structures shows that the LYS element predomi-nantly regulates either single lysC and lysA genes, or a composite operon encoding the lysine biosyn-thesis genes . In the genomic search for new lysine-regulated genes, three new types of ly-sine transporters, namely LysW, YvsH and LysXY, were identified . The predicted func-tion of the LysW transporter was validated in a subsequent study.
|Phylum||Regulog||RNA regulons (studied genomes)||RNA sites|
|Firmicutes||Lysine - Bacillales||11 (11)||23|
|Firmicutes||Lysine - Clostridiaceae||19 (20)||38|
|Firmicutes||Lysine - Lactobacillaceae||15 (15)||25|
|Firmicutes||Lysine - Staphylococcaceae||7 (7)||15|
|Firmicutes||Lysine - Streptococcaceae||2 (15)||4|
|Proteobacteria||Lysine - Enterobacteriales||5 (12)||5|
|Proteobacteria||Lysine - Pasteurellales||8 (9)||10|
|Proteobacteria||Lysine - Shewanellaceae||16 (16)||35|
|Proteobacteria||Lysine - Vibrionales||10 (10)||22|
|Thermotogae||Lysine - Thermotogales||9 (11)||9|