SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). It was first discovered in the marine bacterium Candidatus Pelagibacter ubique and can also be found in marine metagenomes.[1] SAM-V features a similar consensus sequence and secondary structure as the binding site of SAM-II riboswitch, but bioinformatics scans cluster the two aptamers independently. These similar binding pockets suggest that the two riboswitches have undergone convergent evolution.[2]
| SAM-V | |
|---|---|
Conserved secondary structure of the SAM-V riboswitch.
| |
| Identifiers | |
| Symbol | SAM-V |
| Rfam | RF01826 |
| Other data | |
| RNA type | Cis-reg; Riboswitch; |
| Domain(s) | Marine metagenome |
| PDB structures | PDBe |
SAM-binding was confirmed using equilibrium dialysis. The riboswitch has been characterised as a 'tandem riboswitch' - it is able to regulate both translation and transcription. When SAM is present in high concentration, SAM-II will bind its ligand and form a terminator stem to halt transcription. If SAM exists in lower concentrations, SAM-V will be transcribed and, if SAM concentration should then increase, it can bind SAM and occlude the Shine-Dalgarno sequence of the downstream open reading frame. This regulation controls parts of the sulfur metabolismofmarine bacteria.[2]
The crystal structure of the riboswitch has been solved (PDB 6FZ0). It contains a pseudoknot.[3]