Collection of regulogs for GEMM_RNA_motif (RF01051) RNA regulatory element
The Cyclic di-GMP riboswitch, also known as GEMM RNA motif, is a highly conserved RNA structure that is involved in regulation of a large variety of microbial processes including virulence, motility, and biofilm formation. It serves as a riboswitch that binds directly to cyclic di-guanosine monophosphate . Cyclic di-GMP is a second messenger used in signal transduction in a wide variety of bacteria. Cyclic di-GMP is synthesized by proteins with diguanylate cyclase activity.
Cyclic di-GMP riboswitch was originally identified by bioinformatics as a conserved RNA-like structure called the "GEMM motif" .
These riboswitches are present in a wide variety of bacteria, and are most common in Firmicutes and Proteobacteria (most commonly in Gamma- and Delta-proteobacteria). The genomes of Geobacter species predicted to have from 4 to 28 instances of this riboswitch.
The solved crystal structure of the cyclic di-GMP riboswitch from the tfoX gene from Vibrio cholerae showed that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking .
|Phylum||Regulog||RNA regulons (studied genomes)||RNA sites|
|Cyanobacteria||GEMM_RNA_motif - Cyanobacteria||2 (14)||6|
|Deinococcus-Thermus||GEMM_RNA_motif - Deinococcus-Thermus||1 (5)||3|
|Firmicutes||GEMM_RNA_motif - Bacillales||7 (11)||9|
|Firmicutes||GEMM_RNA_motif - Clostridiaceae||12 (20)||29|
|Proteobacteria||GEMM_RNA_motif - Enterobacteriales||1 (12)||1|
|Proteobacteria||GEMM_RNA_motif - Ralstonia||1 (6)||1|
|Proteobacteria||GEMM_RNA_motif - Shewanellaceae||13 (16)||20|
|Proteobacteria||GEMM_RNA_motif - Vibrionales||10 (10)||15|
|Proteobacteria/delta||GEMM_RNA_motif - Desulfovibrionales||3 (10)||5|