| 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-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-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 metabolism of marine bacteria. [2]
The crystal structure of the riboswitch has been solved (PDB 6FZ0). It contains a pseudoknot. [3]
See also
References
- ^ Meyer MM, Ames TD, Smith DP, et al. (2009). "Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'". BMC Genomics. 10: 268. doi: 10.1186/1471-2164-10-268. PMC 2704228. PMID 19531245.
- ^ a b Poiata E, Meyer MM, Ames TD, Breaker RR (November 2009). "A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria". RNA. 15 (11): 2046–2056. doi: 10.1261/rna.1824209. PMC 2764483. PMID 19776155.
- ^ Huang, Lin; Lilley, David M J (27 July 2018). "Structure and ligand binding of the SAM-V riboswitch". Nucleic Acids Research. 46 (13): 6869–6879. doi: 10.1093/nar/gky520. ISSN 0305-1048. PMC 6061858. PMID 29931337.
Further reading
- Kazanov MD, Vitreschak AG, Gelfand MS (2007). "Abundance and functional diversity of riboswitches in microbial communities". BMC Genomics. 8: 347. doi: 10.1186/1471-2164-8-347. PMC 2211319. PMID 17908319.
- Zhu Y, Pulukkunat DK, Li Y (2007). "Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes". Nucleic Acids Res. 35 (7): 2283–2294. doi: 10.1093/nar/gkm057. PMC 1874661. PMID 17389640.
- Winkler WC, Breaker RR (2005). "Regulation of bacterial gene expression by riboswitches". Annu. Rev. Microbiol. 59: 487–517. doi: 10.1146/annurev.micro.59.030804.121336. PMID 16153177.
- Mandal M, Lee M, Barrick JE, et al. (October 2004). "A glycine-dependent riboswitch that uses cooperative binding to control gene expression". Science. 306 (5694): 275–279. Bibcode: 2004Sci...306..275M. doi: 10.1126/science.1100829. PMID 15472076. S2CID 14311773.
- Yooseph S, Sutton G, Rusch DB, et al. (March 2007). "The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families". PLOS Biol. 5 (3): e16. doi: 10.1371/journal.pbio.0050016. PMC 1821046. PMID 17355171.