SAM-V riboswitch

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
SymbolSAM-V
RfamRF01826
Other data
RNA typeCis-reg; Riboswitch;
Domain(s)Marine metagenome
PDB structuresPDBe

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
  1. 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.
  2. 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.
  3. 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
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