Glycine riboswitch

The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist of two metabolite-binding aptamer domains with similar structures in tandem. The aptamers were originally thought to cooperatively bind glycine to regulate the expression of downstream genes. In Bacillus subtilis, this riboswitch is found upstream of the gcvT operon which controls glycine degradation. It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation.[1]

Glycine
Consensus secondary structure and sequence conservation of Glycine riboswitch
Identifiers
SymbolGlycine
RfamRF00504
Other data
RNA type Cis-reg; Riboswitch
GOGO:0006545
SOSO:0000035
PDB structuresPDBe

The originally discovered, truncated version of the glycine riboswitch exhibits sigmoidal binding curves with Hill coefficients greater than one, which led to the idea of positive cooperativity between the two aptamer domains.[1][2] Data in 2012 shows that cooperative binding does not occur in the switch with its extended 5' leader, though the purpose of the switch's dual aptamers is still uncertain.[3]

Atomic resolution structures of portions of glycine riboswitches have been obtained by X-ray crystallography.[4][5]

In vivo experiments demonstrated that glycine does not need to bind both aptamers for regulation. Mutation to the first aptamer caused greatest reduction in downstream gene expression, while mutation to the second one had varying effects. Glycine-induced expression of the gcvT operon is needed for B. subtilise growth, swarming motility and biofilm formation (in high glycine environment).[6]

References
  1. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (October 2004). "A glycine-dependent riboswitch that uses cooperative binding to control gene expression". Science. 306 (5694): 275–279. doi:10.1126/science.1100829. PMID 15472076. S2CID 14311773.
  2. Kwon M, Strobel SA (January 2008). "Chemical basis of glycine riboswitch cooperativity". RNA. 14 (1): 25–34. doi:10.1261/rna.771608. PMC 2151043. PMID 18042658.
  3. Sherman EM, Esquiaqui J, Elsayed G, Ye JD (March 2012). "An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches". RNA. 18 (3): 496–507. doi:10.1261/rna.031286.111. PMC 3285937. PMID 22279151.
  4. Butler EB, Xiong Y, Wang J, Strobel SA (March 2011). "Structural basis of cooperative ligand binding by the glycine riboswitch". Chemistry & Biology. 18 (3): 293–298. doi:10.1016/j.chembiol.2011.01.013. PMC 3076126. PMID 21439473.
  5. Huang L, Serganov A, Patel DJ (December 2010). "Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch". Molecular Cell. 40 (5): 774–786. doi:10.1016/j.molcel.2010.11.026. PMC 3726718. PMID 21145485.
  6. Babina AM, Lea NE, Meyer MM (October 2017). "Bacillus subtilis". mBio. 8 (5). doi:10.1128/mBio.01602-17. PMC 5666159. PMID 29089431.
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