Collection of regulogs for SAM (RF00162) RNA regulatory element
The SAM riboswitch, also known as S-box, is a highly conserved RNA structure that is involved in regulation of methionine and cysteine metabolism in Bacteria. S-box serves as a riboswitch that binds directly to S-adenosylmethionine (SAM) to regulate gene expression via attenuation of transcription using formation of alternative secondary structures in the S-box region [10094622, 12702767, 12910260]. SAM is a common co-substrate involved in methyl group transfers and is synthesized from the methionine amino acid by the SAM synthase MetK.
The alignment of 100 S-box leaders confirms high degree of conservation of the S-box primary and secondary structure .
The S-box consists of five conserved helices, and single-stranded regions, and a pseudoknot structure formed by pairing between the end loop of helix P3 and the interior loop between helices P4 and P5 (Fig. 5). The solved x-ray crystal structure of the SAM riboswitch complexed with SAM has confirmed the predicted secondary structure of riboswitch and showed the four-way junction organization, with two sets of coaxially stacked helices arranged side-by-side and a pseudoknot formed between a stem loop and the a helix joining region [16810258, 18205390].
Search for S-boxes and analysis of operon structures identified a large number of new candidate methionine-regulated genes in various bacteria, mostly Firmicutes . In the genomic search for new methionine-regulated genes, several new types of candidate methionine transporters including MetT amd MtsABC were identified .
|Phylum||Regulog||RNA regulons (studied genomes)||RNA sites|
|Actinobacteria||SAM - Corynebacteriaceae||1 (8)||1|
|Chlorobiales||SAM - Chlorobiales||11 (11)||14|
|Chloroflexi||SAM - Chloroflexia||5 (5)||14|
|Cyanobacteria||SAM - Cyanobacteria||2 (14)||2|
|Deinococcus-Thermus||SAM - Deinococcus-Thermus||5 (5)||9|
|Firmicutes||SAM - Bacillales||11 (11)||98|
|Firmicutes||SAM - Clostridiaceae||19 (20)||72|
|Firmicutes||SAM - Lactobacillaceae||2 (15)||2|
|Firmicutes||SAM - Staphylococcaceae||7 (7)||40|
|Proteobacteria/delta||SAM - Desulfovibrionales||4 (10)||4|
|Thermotogae||SAM - Thermotogales||1 (11)||1|