| 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. 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.
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.
The crystal structure of the riboswitch has been solved (PDB 6FZ0). It contains a pseudoknot.
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.
- ^ 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.